[[ New Game ]]
"CAUTION!!" - Utsuho Reiuji's banners.
Special Thanks: Nintendo. S Presents: TOUHOU - Based on Mother 1 intro.
"Junya Itoi" - Combination of Junya Oota, ZUN's name, with Shigasato Itoi, creator of Mother.

[[ Hakurei Shrine ]]
"*hop* I'm a frog('s hat). Do you want me to record everything that's happened so far?" - Save frogs in Mother 3 say the same thing minus the parentheses.

[[ Garden of the Sun ]]
"Cirno brandished her watermelon blades!" - In Advent Cirno, a Final Fantasy 7 parody, Cirno wields watermelon blades. For some reason.
"So let us not waste our time in idle discourse!" - Waiting for Godot. Not as wonderfully ironic as it was there, but still rather appropriate.

[[ Meteor Crossing ]]
"There are ants at your feet. You might accidentally step on them, so please don't go over there." - Ants restrict your path in a couple places in Mother 3.

[[ Scarlet Devil Mansion - Patchouli's Room ]]
"I came across some foreign beverages. I got this thing called a Big City Cola." - Item from Mother 3. In New Pork City, I think.
"I wasn't exactly planning on coming here to take it easy, but..." - I'm not pointing out every instance of "take it easy." Google Yukkuris. Orrr maybe you shouldn't.
"Masked Maid Girl" - Kamen no ("Masked") Maid Guy.
Tarot card - "The World" Yu-Gi-Oh card, which apparently has an effect similar to Sakuya's attack. (Also, ZA WARUDO.)
"Patchouli is coughing violently!" - Reminiscent of Porky doing nothing helpful as a helper at the beginning of Earthbound.
"Patchouli cast Healall!" - Dragon Quest healing spell.
"Got the Dream Diary." - Possibly Yume Nikki (which translates to Dream Diary). But that's basically the only connection.
"...There we go. Fixed aaall up." - Dr. Saturn from Earthbound.
"A sound flowed from the mask! Reimu remembered the melody." - The melodies are from Mother 1, also usually found in random objects.
"...Marisa. This seems it may be an affair of unprecedented weight..." - Imperishable Night loading screen: "This incident is unprecedented serious affair."

[[ Scarlet Devil Mansion - Entrance ]]
"Basement. Beware of Monster Houses." - Roguelikes typically involve going down floors, and some feature Monster Houses where swarms of enemies suddenly appear.

[[ Path to the Scarlet Devil Mansion ]]
"Idiot Lake. (Translator's note: Idiot means baka.)" - Actually the Lake of Mist, but anyway. Supposed Death Note subbing that said "All according to keikaku. (Translator's note: Keikaku means plan.)"

[[ Yukari's House ]]
"If you came expecting the same treatment I would give Reimu, that is simply tooooo bad." - Ness's mom says "Well, TOOOOO BAD!" to Porky not liking your favorite food.
"Is it OK desu ka for me to proceed?" - "OK desu ka?" ("Is this okay?") is a sound clip from Itoi himself used in the Earthbound and Mother 3 naming screens.
"Do you have say, a pad of paper ready?" - The rock in the Lost Underworld of Earthbound, who says you "may need to take notes."
"I am such a hero! ...Well, the friend of a hero, at least. Fufufu." - The first time you call Dad in Earthbound, he says "I'm such a hero! What? Well, the father of a hero, at least. Wa ha ha!"
"But, uh... This is getting unusually serious. No time to wait warmly, that's for sure." - Perfect Cherry Blossom loading screen: "Please wait warmly until it is ready."

[[ Yuyuko's House ]]
"Take it from me, if you dare..." - Your Sanctuary bosses in Earthbound. Who also guarded melodies, of course.
"Anubis, meet Roukanken!" - Roukanken is her usual sword, Anubis is from Jojo's Bizarre Adventure.
"You lost a trial of guts, kid." - The Imperishable Night extra stage is referred to as a "trial of guts" by Reimu.
Yuka's Luffy hat - Uh... yeah. It's Luffy's hat from One Piece.
"I nabbed it on the way from some guys who were calling themselves pirates." - See above.

[[ Yukarispace ]]
Friend's Yoyo - (Very likely) Ness's yoyo, obtainable in the playroom in the Thunder Tower of Mother 3 if you beat Miss Marshmallow.

[[ Forest of Magic - Marisa's House ]]
"The wing that flaps in the dark!" - Darkwing Duck is "the terror that flaps in the night." Mystia? Not so much.
"Tondagossa!" - The DCMC's catchphrase from Mother 3.
"If by the tiny, tiniest of chances we lose..." - Nazrin's theme, A Tiny, Tiny, Clever Commander.
"Just go home and play your easy mode." - IOSYS's Overdrive animation: "Easy mode?! HOW WEAK."
"Stone! Sheet! Clippers! You DEAD! ...Maaaybe." - The Nowhere Island version of Rock Paper Scissors, played with the DCMC to determine Duster's fate in Mother 3.
"My teacher. May the beautiful Mima rest in peace for all time." - Hinawa's grave in Mother 3.
"Boom." - Policenauts fan translation. The original word in both games really just means "wrong," but it sounds so much cooler, even in the wrong context.

[[ Mother 3 Love Theme ]]
"Yes, that's sooooo." - Rumia (the "black one" just mentioned)'s catchphrase is the childish-sounding "Is that sooo?"
"YEAAAAAHHHHHHHHHH!! FAL-CON! PAUUUUUUUUUUNCH!" ... "YES!" - Captain Falcon in Super Smash Bros.
"You smell just like Mom..." "Huh? You don't mean that smelly sunflower stuff, do you...?" - Yuka smells like Hinawa. Aww.

[[ Yukari's House ]]
Aya - The photographer who suddenly falls from the sky in Earthbound.

[[ Outside Alice's House ]]
"Soon, I shall become one with the 12th dimension..." - Apparently most of the Alice stuff here is based on Yubel from Yu-Gi-Oh GX.
"A magician like me can't understand such matters. Do I make the "lo" and you make the "ve"?" - In Discworld, magicians say "the sound of one hand clapping" is "cl; the other hand makes the "ap.""
"N-Now... it's a d-d-d... duel...!" - Further Yu-Gi-Oh shenanigans.
"Alice (Sick) played the Magic Card "Europe"!" - Guessing the same. (Apparently they're called "spellcards" in English, which is... amusing, to say the least.)
"I'm the BEST!!" - Not exactly a reference, but I imagine this being said like Jecht from Final Fantasy X.
"Gahahahahahahahaaa!" "Ahahahahahahahaaa!" "Gahahahaha, gahahahahaaa! Gahahaha, gahahaaa! Hoo." - Maniacial laughter from Revenge of Meta Knight in Kirby Super Star.
"Hey, it's my doll!" - Resident Evil 4: "Hey, it's that dog!"

[[ Human Village ]]
"...I came to deliver this supply of Pencil Rockets to the village children." - Attack item from Mother 3.
Nailgun - "Um, caved...?" in the description comes from a weird meme involving dirty, dirty Keine.
Mind Bullets - Wonderboy by Tenacious D. (Additionally, the description is "Kills yaks dead. That's PSI, Marisa.")
Wooden Shield - Legend of Zelda, particularly the description: "It's safe to go alone with this," reflecting "It's dangerous to go alone! Take this" for the wooden sword.

[[ Bamboo Forest - Cutscene ]]
Rhythm Emotion - Some Gundam opening theme.
"No idea what you're talking about, but cool story, miko." - Cool story, bro.

[[ Outside Eientei ]]
"Eirin produced the Broken Bazooka and slowly pulled the trigger." - One of the broken items in Earthbound Jeff can fix.
"Help us, Yuka-rin!" - IOSYS's "Help me, Erinnnnnnnnnn!"

[[ Forest of Magic - Marisa's House ]]
There's a ship from R-Type outside Marisa's house. - There's a ship from R-Type outside Marisa's house.
"Hello! And... goodbye!" - Teleporty Moonside surfer guys from Earthbound. (And the Beatles, but yeah.)
"I name it... the R-9N (for Nitori)!" - Based on R-Type ship naming scheme.
"This is Mother, after all. So it's gonna have to crash, right?" ... "A refrigerator'd fly more safely." - Most Mother vehicles crash, but the refrigerator in Mother 3 actually doesn't do too bad.
"...But man, I worked through the night on it, so I was kinda hoping you would." - Jeff fixes items by "working through the night."
"You are the biggest pansy." - You're one to talk, flower girl.
"Got a Laser Crystal. Got a Power Capsule." - R-Type and Gradius powerup things.
"Oooops!" - General screwup message from Wizardry.

[[ Youkai Mountain ]]
"Wonder if I can buy Suguri here..." - It's a game. That's all I know and probably all that really needs to be said here.
"Still no Bonobono 31...?" - Evidently there have been only 30 for a long time.
"Sometimes, the S.S. Komachi Special comes along here." - Komachi's boat, featured in one of her attacks in Scarlet Weather Rhapsody, is commonly called the "S.S. Komachi Special."
"Hey, you, eat curry." - Apparently a 2ch meme of some sort.
"You don't have the proper clothes to wear to go clothes shopping." - See above.
"Wild MISSINGNO. appeared!" - Glitch Pokemon from Pokemon Red/Blue/Yellow.
Koitsu and Kid Dracula - Characters from Parodius. (The former translates to "this guy," just so you know.)
"Speed Up!" - Sound effect for, well, speeding up in Gradius.
"Battle Garegga," "Dodonpachi," "Image Fight," "why is Cho Aniki in an arcade?" - All shooters.

[[ Nitori's House ]]
"Ah, but Marisa, making it out okay even if you crash is Nitori quality." - "(That is) VIP QUALITY" is a common thing on 2ch, whose users call themselves "VIPPERs."
"...Gah! Youkai?!" - Nitori's first line in Mountain of Faith is "Gah! Human?!" (Or close to that, anyway.)
"Buh? I don't drink your cucumber-flavored beer, though." - IOSYS's "You Should Drink Cucumber-Flavored Beer!"
"Zeh? Shoot." - The bullet, am I right?
"Mari strong! You, go me! SMAAAAAASH dudes?" - Sort of Ayla from Chrono Trigger. (Particularly her leaving off the last syllable of Crono's name, though that's only in the Japanese version.)
"It's called a Tanetane Island Mushroom. You gonna eat it? You gotta be interested, right?" "...Uh, I DO know what they do, actually." - Mother 3's Tanetane Island's psychadelic mushrooms.
Super Mushroom - It's a Super Mario Bros. mushroom. It makes you big.
"Alright! Time for Monster Hunter Nitori to get crackin'!" "Our objective: suppressing youkai!" - Monster Hunter.

[[ Inside Youkai Mountain - One Big Hole ]]
"Something gross spurted out! Nitori turned into Rotten Bread." - Roguelikes with trap tiles that make your items unusable. (Or worse.)
"Ah, nooo! Stooop! I'm small, dirty, and not very delicious!" - Mike from Mother 3, who gives out "small, dirty, not very delicious cookies."

[[ Youkai Mountain - Summit ]]
"ENERGY RECHARGE COMPLETED" - The message that energy recharge stations in Super Metroid give. In fact, they ARE energy recharge stations from Super Metroid.
"If you're interested, though, go look for a Japanese game called Ginga no San-nin!" - Well, it's true.
"Objective completed! Returning to the village in 20 seconds." - Monster Hunter quest completion message.
"Miss Iku extended a heavenly garment to attack! Bravo!" - Bravoman.
"Miss Iku attacked with a drill! Drillululululu!" - Gurren Lagann.
Bomb - The sprite is from Bomberman.
"You got the booooomb! (Said to Zelda item jingle.)" - Yeah.

[[ Youkai Mountain - Hole ]]
"A strange enemy is blocking the way!" - This whole thing is basically the same situation as Tanetane Island in Mother 3.

[[ Mountainside ]]
"Marisa, Master Marisa, your family is waiting... Gwaaaaargh!" - Department Store Spook from Earthbound.

[[ Mountainside - Summit ]]
"Miss Ikuuu... It hurts... It huuurts... I'm... sad... Miss Ikuuu..." "Ahhh... ahhh... ooh... I feel... good... Miss Ikuuu..." - Giygas from the end of Earthbound.
"Gyokkooooowwwwww! It's super-effective!" - Message for type-weakness attacks in Pokemon.
"Bzzzt! Even from oarfish!" - "Bzzzt! Even in Dream!" was a preliminary translation of the song during Salsa's dream in Mother 3.
"Reimu suffered major damage. Reimu couldn't stand up." - What happens to Flint when he gets hit in the ending of Mother 3.

[[ Youkai Mountain Other Summit ]]
"Welcome to Moriya Shrine. Wecomel to Shoriyamine." - "Welcome to Moonside" messages from Earthbound.
"Wa-hey! Nitori's gonna have to juuump!" - Sounds pretty dangerous, Nitori. No... sounds Dangeresque.

[[ Moriya Shrine ]]
"Curry of the flame! Superspicy curry!" - Item in Super Smash Bros. Brawl.
"Come on, already! Who (the hell) do you think I am?!" - Gurren Lagann.
"Fuzzy Pickles! (Woof!)" - Earthbound cameraman's catchphrase, or whatever. Also, I seem to remember a "reverse-monkey" like that somewhere in Earthbound.
Five missiles to open a red door - Standard procedure in a Metroid game.

[[ Moriya Shrine - Some Cliff ]]
"...Strange, isn't it?" - Not appropriate at all, but Sonic the Movie:
"You might know everything I'm going to do, but that's not going to help you, since I know everything YOU'RE going to do! STRANGE, ISN'T IT?!"
"Hmph. Freakin' spacenoids, I tell you." - From the Cho Marisa page: "My dear, weak spacenoids!"

[[ Moriya Shrine - Inside? ]]
"Run that by me in English." ... "Say WHAT again?!" - Pulp Fiction.
"Yikes, you work fast!" - Final Fantasy V, after Butz has a dream about Cid and Mid finishing the airship and wakes up to find it's true.

[[ Moriya Shrine ]]
"It's too cold." "I'm afraid of heights." "I ain't goin'." "...You chickens." - Revenge of Meta Knight in Kirby Super Star, when Kirby's in the windy area under the ship.
"The Hakurei Shrine gave its final breath." "Reimu... Nitori is really absent-minded, that's true. You'll forgive that absent-minded kappa, won't you?" - Claus's death in Mother 3.

[[ Crossroads ]]
"For some weird reason, an octopus-shaped statue is blocking the path." - The pencil statue in Earthbound was an octopus one in Mother 2.

[[ Starman Hideout - Lab ]]
"Why, why, why, I wondered... Why did I want so much for you alone to be at my side...?" - IOSYS's Marisa Stole the Precious Thing: "Why why why don't I miss you a lot forever?"

[[ Eientei - Reisen's Room ]]
"A Suppository of Life should do the trick." - The Cup of Lifenoodles and Life Gum in Earthbound, only Reisen-style.
"...It'll take some time before it reaches the affected area so, aah, you know." - IOSYS's "It Doesn't Stop at the Affected Area, But Goes Deep Inside and Aah Aaahn ~ The Final Udongein."

[[ Eientei ]]
"This chair. This chair. This chair. This chair!" (Placed by me in the maze to make it ever-so-slightly more entertaining.) - Tsukihime.

[[ Eientei - Eirin's Room ]]
"V-1969": Short for Voyager 1969, the Imperishable Night Stage 6 music.
"Neo Phase Distorter Version XXAY!" - The Phase Distorter from Earthbound, of course.

[[ Moriya Shrine - Mission Briefing ]]
Let's just get this out of the way - Sanae's whole scenario is pretty much a Metroid Fusion parody with Sanae as Samus and Suwako as Adam. So I'll leave most of those out.
"Sanae Kotian" - Sanae Kotiya + Samus Aran. Oh, and though it doesn't come across in English, Suwako often puts Sanae's first "Sa" in Katakana, as if she's saying "Sam... nae."
"If you were so unfortunate as to take on Porky right now, >you would certainly lose the fight.<" - Might actually be an exact line from Fusion about Samus challenging the SA-X.

[[ Youkai Mountain ]]
"Metroid Dread is nearing completion. Really." - A rumored new 2D Metroid game that's been floating around a while. Possibly even referring to the Earthbound 2 sign in Fourside.

[[ Thunder Tower ]]
"Wanna do it?" - Uhhhhh
"Ah, welcome to Bourbon House." - 2ch meme. I changed up all the other instances of it, though.
"Hoooh... cutie... I'll take ya home with me... Sorry, I actually don't know anything about Higurashi." - Neither do I, but hey, Higurashi no Naku Koro ni.
"Aren't you getting tired? Be a good girl and get comfortable with me." - Sanae is a good girl.

[[ Thunder Tower - Meeting Room ]]
"Hmm... [the TV] could use a more appealing name... Got it! Just call 'em Happy Boxes!" - Porky/Fassad does the same thing in Mother 3. Well, S is kinda assuming they're actually TVs, but...
"What's this box? There's... no one inside it, is there?" - Finale of School Days: "There's... no one inside you, is there?"

[[ Underground Passage ]]
Warp Star - Kirby.

[[ Meteor Crossing ]]
"These octopus statii are arranged in the Imperial Cross formation." - A formation in Romancing SaGa 2. (Also, grammar!)

[[ Scarlet Devil Mansion - Entrance ]]
"I said it got destroyed because I said there was a freak refrigerator accident, vaa." - Vaa is... SOMEBODY's catchphrase in Lucky Star, apparently.
"Porky. A man of most violent tendencies." - Samus's monologues in Metroid Fusion. I'm pretty sure this one isn't based on any in particular, though.

[[ Path to Scarlet Devil Mansion ]]
"Miss Iku cast Zoom!" - Dragon Quest warp spell.

[[ Thunder Tower - Lobby ]]
"Good... Sanae?" - Good Sonic, you look kinda cool! Alternatively, Sanae is still a good girl.
"Now, Sanae. Your mission ends here. We'll leave the rest to Kanako, and you'll withdraw." - Almost directly from the scene after finding the Metroids in Fusion. Other nearly-copied lines:
"Are you joking?! Doesn't Lady Yasaka know how dangerous Porky is?"
"And all the hag'll say on the matter is that "it is not necessary that you understand us.""
"Oh, to only return to the outside world... Isn't it nice to think about?" - I admit it, I intended it to be the last line of The Sun Also Rises.
But it turns out that's actually "Yes... Isn't it pretty to think so?" I like it how it is, though, so I'm not changing it. ANYWAY, back to Fusion quotes.
"...Fools..."
"If Porky and Kanako are working together, they'll be able to earn the faith of Gensokyo's entire population. [etc.]" - Samus's monologue about what the X will do to the universe.
"Sanae! Do you REALLY think that'll do any good, girl?!" - Sanae is still a good girl.
"Well, then, what WOULD this "me" you knew do now?"
"And do it promptly. Any objections, lady?"

[[ Thunder Tower ]]
Megamarisa - Comes out of a Megaman X Dr. Light capsule with the proper music.
"Live-A-Live downloaded. You feel like kicking the CRAP outta evil!" - The Japanese-only (though fan-translated) RPG Live-A-Live. Ends with a battle against the timeless embodiment of evil, basically.
"Dirty Sign used Hyper Bomb!" - Street Fighter III.

[[ Generator Room ]]
"But point is, I'm the number two of Gensokyo." - You sure are, Tenshi. You sure are.
"Did you think it'd be such a pop-shoot-bang job?" - Orange from Lotus Land Story: "I'll pop, shoot, and bang your head off!" (At least, the Touhou Wiki translation.)
"This time, I've got a repli... I mean, original Rainbow Sword, borrowed from Mr. Kirby himself." - Kirby's weapon against the final boss of Kirby's Dream Land 2.
"I will become the Messiah! Haahaahaa!" - Omega's (still-Japanese) voiced line before you fight him in Megaman Zero 3.
"Tenshi used Sun Render with the Rainbow Sword!" - Yu-Gi-Oh GX. Of some sort.
"Aether! HYAAAH!" - Ike from Super Smash Bros. Brawl.
Tenshi was defeated! ...Oh, wait. - Mother Brain's dino-revival after being defeated in Super Metroid; also appropriate because of Tenshi's revival in SWR.
"Tenshi tried Scarlet Weather Rhapsody of All Humankind!" - Her final spellcard in Scarlet Weather Rhapsody (again, used after her revival).
"Miss Iku did the Hustle Dance!" - Dragon Quest healing dance.
"Suddenly, Miss Iku jumped out in front of Sanae! Miss Iku took mortal damage! Miss Iku couldn't stand up." - Flint's sacrifice from the end of Mother 3.

[[ Former Hakurei Shrine ]]
"Good mooorning, princess!" - Life is Beautiful.
"Turtleee!" - Exdeath versus Ghido in Final Fantasy V.

[[ Outside Mugenkan ]]
"Elly threw a scythe!" "Elly threw a floor tile!" - Well, that IS what she does in Lotus Land Story.
"I couldn't help it! I couldn't help it!" - Elly's comment on Marisa/Reimu having priorly defeated her to the other.

[[ Mugenkan - Table ]]
"And "Ahaha, just because I'm the first stage boss, you shouldn't underestimate me!"...?" - Quoting Orange, the first boss of Lotus Land Story, to refer to her.
"Poor her." - As Touhou Wiki's page on her says, poor Orange.

[[ Mugenkan - Bedroom ]]
"That night, Marisa had a dream." - Very much like Chapter 6 of Mother 3.

[[ Desert Cave ]]
"Desert Cave: Level 58." - Probably supposed to be roguelikes. Who knows.
"Also, caves are great." - In a few of the comments on Subterranean Animism songs, ZUN says "caves are great." ...Well, they are!
a - A default enemy in the RPG Maker runtime package graphics. Same for the music. Also maybe a reference to Negativeman from Mother 3, at least in his first appearance.

[[ Desert Cave - Severed Head ]]
"I am a severed head." - It's Poo from Earthbound's, to be specific.

[[ Desert Cave - Exit ]]
"My name's Page." "Jones." "Plant." - Apparently a Jojo's Bizarre Adventure reference.
"Prepare for an all-out attack!" - Persona 3.
The Ultimate Combo - Hitting nine or more enemies with a shell in Mario games to get 1-ups.

[[ Outside Castle ]]
"The color's weirding me out the most, though. It's some kinda mix of NES and SNES." - Mima's castle is a recolor of Queen Mary's from Mother 1.

[[ Castle ]]
"A Shinto priest has written some grateful words here." - ZUN is commonly known as "the Shinto priest."
"A youkai. Yes. Youkai moe. [etc.]" - ZUN's comments on Yuka from Kioh Gyoku, the Seihou game where she appeared.
"We put a youkai there in advance. Definitely MOE." - The end of IOSYS's FOE video.

[[ Castle - Mima's Room ]]
"There was a human who came in from the outside world, too... But I think she was poisoned by a strawberry or something." - Okazaki's theme is "Strawberry Crisis."
"...Who the HELL do you think you are?!" - NOT a(n intentional) Gurren Lagann reference, geez! (There's been enough of them already.)
"You're a goddamn PHONY!" - NOT a Catcher in the Rye reference, period, geez! (Seriously, I like that book and all, but I use "phony" without intending to reference it pretty often.)

[[ Castle ]]
Only God - Entei from Pokemon Gold/Silver/Crystal. With a black bar over the eyes, because otherwise, copyright infringement.
"Hell no. Shut up and go sleepy-bye, you green Ghostie." - Baby Bowser from Yoshi's Island: "I wanna go sweepy-byyye!!!" "What kind of gween donkey is dat?"

[[ Path Out of Desert Cave ]]
"Say password." "Wait three minutes." - In Earthbound, the password to enter Belch's base was literally waiting three minutes.

[[ Saturn Valley ]]
"I believe the morning sun." - First line of the lyrics to Pollyanna.
Sword of Kings - Really rare, only weapon for Poo which you could only get at one point in Earthbound, now made free and nigh-useless.
"Hear phone. Who was phone?" - But Okazaki is dead. THEN WHO WAS PHONE?
"Then, the faraway... the science... was.... raised me up... ...was... amazing..." - All based on Merlon's sleep-inducing speech in Paper Mario about how he got his powers.
Zexonyte - Material needed to make the Phase Distorter work in Earthbound, obtained from the meteorite since it can't be found on earth.

[[ Makai - Midpoint ]]
"Have you heard that my laser is not difficult? You heard very, VERY wrong, ze." - "Laser is not difficult" typically precedes an explanation of how to use Master Spark.

[[ Makai - Stage 6 ]]
"And MUCH less TETRICE." - Not exactly a reference, but it's the continuation of "once, twice, thrice."
"With this Gungnir...! I shall run you through!" "Underestimate not the power of the gods!" - Valkyrie Profile 2.
"Lady Shinki used Hairspray Hammer!" - Referring to her stray hair strand sticking out. (The Japanese term is "ahoge.")
"Lady Shinki used the Exploding! God! SLAAASH!" - G-Gundam.
"OH, WHAT THE." - SirRonLionHeart. PK SUPERB ULTRA OMEGA.
"Let me send you to them with my Mother Power." "Shinki sent Reimu back along a trail of bread crumbs." - Bread crumbs in Mother 1 allowed you to warp back to the start of the crumb trail.
"Well, do your best, now." - Not even intentional, but I suppose "girls do their best now and are preparing" from several Touhou loading screens.

[[ Saturn Valley ]]
"I've deposited 100,000 Gald into your bank account." - Gald is the currency in the Tales games.

[[ Saturn Valley - Landing Site ]]
"You've traveled very far from home." - Earthbound coffee break.
"May the goddess of fate smile upon you..." - The original line from the end of the Mother 2 coffee break, changed to "I wish you luck..." in Earthbound.
"Gensokyooooo! I'm hooooome!" "...Is this a sitcom or something?" - Honey, I'm hooooome!
"Perhaps you're Ichigo Kamen?" "...Huh? Itchy who?" "...Never mind. She must be rubbing off on me." - My masterful handling of S's original obscure reference.
"So, is she gonna replace you?" "I'm going to hit you as hard as I can." - Fight Club.
"..."Why? Why? Why doesn't Marisa look at me, forever?", I always thought." - Again, IOSYS's Marisa Stole the Precious Thing.
"Go ahead! Make my day!" - Sudden Impact.
"Climb up! And get the last chance!" - Name of an F-Zero song. Since she's Captain Falcon and all.
Giro-Blame - Another enemy from Ginga no San-nin, like Galbangor.

[[ Snowhou ]]
Narpas Sword - NARPAS SWORD0 000000 000000 is a password that gives you special benefits in the original Metroid, supposedly standing for North American Release Password.
"What a cute little frog... FOR ME TO STOMP ON." - Slightly less rude version of Triumph the Insult Comic Dog's "...for me to poop on!", though now that I think of it, somewhat improbable for Mima.

[[ Snowhou - Fairy-a ]]
Snowwoman - Snowman from all the Mother games mixed with Letty's theme, Crystallized Silver.
"Who and who? Pokey and Kawasakinaga... Yasaka?" - I see what I did there. As for the other name, Chef Kawasaki from Kirby.
"Okay, snowmanlady." - Haggleman Lady from Retro Game Challenge's Haggleman 3.
Cirno's Unfounded Revenge - Beloved Tomboyish Girl + Unfounded Revenge from Mother 3.
"Earnest Ice Sword" - Romancing SaGa.

[[ Snowhou - Stepping Snow ]]
"Wahoo!" - Klonoa's favorite yell, appropriate given the Stepping Wind to follow.
"Marisa! What's Mima weak to?!" "Nothing... except jelly donuts." - Also Mokou's greatest fear, at least after Reimu and Yukari say they're terrifying in Imperishable Night Extra.
"I only don't have legs when I'm in Beast Mode." - Transformers Beast Wars.
"Hey, Reimu! Now I'll show you!" ... "You're too SLOOOW!" - Sonic from Super Smash Bros. Brawl.

[[ Outside Kourindou ]]
"If it isn't my old nemesis... A BUILDING!" - Edited Spiderman comics: "My doctor's retarded. I don't have a brain tumor. If it isn't my old nemesis... A TRUCK!"
"Ranta-tan? Who?" - A 2ch ASCII art character who likes to dance while no one's around. Originally "Rintarou," who's a Medabots character, but geez doesn't this game have enough references to that.
"Well, I've heard rumor among the fairies about this "encyclopedia that anyone can edit"... Dunno how well it can be trusted, though." - Wikipedia. (Or perhaps Touhou Wiki.)

[[ Kourindou ]]
"Ohhh, you're into THAT. You only like the girls, don't you...?" - Castle of Shikigami 2: "Ohhh, you're into THAT." "I like girls, but now... it's about justice."
"Got 100 Munny." - Currency in Kingdom Hearts.

[[ New Hinanai City ]]
"The city that's hip and trendy among all the kidz-with-a-z! Welcome to NEW HINANAI CITY!" - Named after New Pork City.
"Don't believe it or still don't believe it, but I'm a healer." - Healers in Earthbound: "Believe it or not, I'm a healer."

[[ Hinanai Tower - Lobby ]]
"Gotta live BIG! If you're a MAN!" - Something from the opening of Medabots.
"Medabot 1... in helmet form." - Gee, I wonder.
"Much like a young inventor, I've been working on it through the nights..." - Jeff works on fixing stuff through the night.

[[ Hinanai Tower - Dungeon Tenshi ]]
"This is Dungeon Tenshi. Anyone who enters, welcome. ...Tenshi" - Brick Road's signs in Dungeon Man. There are a few signs very much like Dungeon Man ones here.
"Yeah, this is a dead end. Why the hell would I give you a present for that? You FAILED." - Dungeon Man DID give you a present for taking a dead end.
"The end seems less dead behind the other door. Wonder why..." - Faced with four ropes in Dungeon Man: "The grass is always greener on the other rope... I wonder why that is..."
"Collect the Stars!" - Donkey Kong Country 2 bonus games.
"Maidens! You must recover!" "Man, Smash Dojo jokes are so out of style!" - Enough said.
"Hey! It's a d-d-d-duel!" - Yu-Gi-Oh.

[[ Hinanai Tower - Tenshi's Office ]]
"Puh-lease. If to err is to be an antiquated human, you are SO erred." - I will concede being somewhat inspired by the Eegra comic: "If to err is human, Too Human is exactly that."
"Look upon 'n' despair, losers." - Tenshi is Ozymandias?
"Bring the meddling hag and her fox here. And their little cat, too." - Scooby Doo.
"Coming from the far west, there are zombies and bats and... Oh, my, it's frightening!" - Zombies and bats and ellipses, oh my!
"(It'd be like fighting the Dragonlord right after Zoma. Not an easy task, you know?)" - Both final bosses of Dragon Quest games.

[[ Scarlet Devil Mansion - Entrance ]]
"Looks like Remilia means business." - The unofficial English name for the first Giygas music in Earthbound, Pokey Means Business.

[[ Scarlet Devil Mansion - Patchouli's Room ]]
"Huzzah! I'm back, Patchouli!" - Balrog from Cave Story. (But not Balrog from Cave Story Wii.)
"Ha-HAH!" - Gene from God Hand.
Strange Patchouli - Strange Klug from Puyo Puyo Fever 2.
"Strange Patchouli chanted Kaboom!" - More Dragon Quest spells.
"I'm Marisa's MOTHER, or at least a spinoff." - Should be self-explanatory.
"And incidentally, Reimu, she was looking for you." - And incidentally, she wants to talk to her about incidents.
Vampire Killer - The start (well, maybe a little earlier) of many Castlevania references. I'll just say most of those to come are evident.
"Well, even if a hardly-problem comes along, we'll whip it, ze!" - If a problem comes along, you must whip it!

[[ Scarlet Devil Mansion - Entrance ]]
"This is an aged world. [etc.]" - Based on the Rondo of Blood intro.
"In the form of a bat, in the form of mist, in the form of a young girl, acting in the deep of night." - While true of Remilia, it's true of Alucard as well. (Well, not young GIRL.)

[[ Blood of Rebirth - Remilia's Room ]]
"I don't like the potential of where this is going." - It's the location of the potential that I don't like.
"Your judgement can say one thing, but the same won't be said of all people! Gensokyo ill needs your twisted justice, ze!" "What is a human? A miserable little pile of excuses..." - Symphony of the Night.
"Count Remilia used Cut-Cut-Cuuut!" - Walachia from Melty Blood sure likes to KATTO.
"Soul Steal!" - Romancing SaGa 2.
"Oh, really?" "Yeah, really." - No wai.
"...Gensokyo ill needs such an idiot." - More Symphony of the Night.
"Data get!" - The classic "Shine Get!" from the Japanese version of Super Mario Sunshine.
Voyager 1969, SaGa 3 Style - Voyager 1969 combined with Magical Tank Battle from Romancing SaGa 3. (Well, more the other way around, really.)
"Well, regardless, for just a grain of a moment, Sanae's hope almost became reality." - Mother 1 Flying Man lyrics: "Life is but a moment, a single grain of sand..."
"Yet Porky, or someone, found them and removed them, almost as if it were just as planned." - JUST AS PLANNED. (Death Note.)
Tenshi defeating Yukari - Depicts the battle system from one of the old Fire Emblems.
"Suppose I gotta do the USUAL thing..." - Ending of Castlevania 1.

[[ Scarlet Devil Mansion - Voile Library ]]
"Girls must be brave, Reimu. I'll be waiting warmly for your success." - Yeah, you've seen this one before.

[[ Hinanai Tower - Lobby ]]
"WARNING! ENEMY SIGHTED WITHOUT AUTHORIZATION!" - Based on the message that repeats after you try to go through a locked door in Sector 6 of Metroid Fusion.
"Miss Sanae ran around really fast!" "Miss Sanae span through the air and tackled!" - Allusions to the Speed Booster and Screw Attack from Metroid.
"Sorry 'bout that. We were just lucky havin' cyborg ninja Reimu Hakurei to help." - The cyborg ninja from Metal Gear Solid.
"Bye, losers. Ever got anything more for me, I'd be SO ecstatic." - She's Tenshi, of course she would be. (Ecstatic Heaven, RAMEEEEE)

[[ Netherworld ]]
"But, oh, I know you people on the other side of that screen well... You won't even dignify me with real words. I KNOW you're saying something like "EX OMG LAWL!"" - EX OMG LAWL
Pitch Black Rumia and her music - Romancing SaGa Minstrel Song, apparently.
"Pitch Black Rumia's attack! [Instant Death] [Moonbeam] [Meteor]" - Fire Emblem.
"Wow, that was really something." - Based on my former translation of "Dude? That's rad." Lame, isn't it?

[[ Yuyuko's House ]]
"Oh, it's juzyou. Zellooooo! Er, I mean... Hellooooo." - Sigma in Megaman X6: "JUZDIE! ZELLOOOOO!"
"Who? Oh, you mean the girl with the nice... er, boat." - "Nice boat." is a meme that started from the not-airing of the finale of School Days, but instead of nice nature scenes and boats.
"What, haven't you ever thrown yourself at the ground and missed?" - The key to flying in the Hitchhiker's Guide to the Galaxy series.
"What ARE numbers?! What IS probability?!" - Cho Marisa page: "What IS amount of energy?! What ARE numbers?! Don't think you can stop the Witch of Love with such things!"
"Strange, there's not a scrap of data on you..." "Sore wa himitsu desu." - Xellos from Slayers, who responds to everything with "that's a secret." It seems surprisingly well-known, but I also added...
"It's a secret to everybody." - Legend of Zelda.

[[ Netherworld ]]
"I despise fools who speak foolishly of foolish things and do them foolishly to such foolish ends." - Franziska von Karma from Phoenix Wright.
"Patchouli chanted "Limbo!"" - MORE Dragon Quest spells.

[[ Muenzuka ]]
"There, there, children. What do you need?" - Apparently a guy at the base of Mt. Itoi in Mother 1.

[[ Shikieki's House ]]
"She looks like a child. And not even one in a high grade, just an elementary kid." - "It's unforgivable to play Easy Mode unless you're an elementary kid, right? HA HA HA HA!! HOW WEAK"

[[ Muenzuka ]]
"DO YOU UNDERSTAAAAAND?!" - Similar enough to Rinbokusan's apparent catchphrase that I just switched it over to the Dragonball Z thing.
"I have come all this way to promote my game, Touhou Kandagawa: fusi a nasan!" - Rinbokusan is from a non-existent Touhou game made up by 2ch. That's about all you need to know.
"Suzuki Rinbokusan" - Oh, and this: her name's actually Sasaki Rinbokusan, but as Kanji-misreading is apparently pretty common with Touhou names (see "Tenko"), she's also called Suzuki.
Company Budget Fourth Movement - Parody of the classical Mr. Passion battle music from Mother 3; also includes part of Phantom Ensemble.
"Because of these two barriers...! I've obtained the power of invincibility! ...Or at least, the barriers have." - Necrophobia, the guy guarding the last save point in Final Fantasy V.
"Rinbokusan tried PK Daddy Alpha!" - Daddycool is sort of a VIPPER (2ch user) mascot, offering invitations to his board of ULTIMATE VIP QUALITY.
"Rinbokusan tried PK Wanna Do It? Beta!" - See prior uhhhhh

[[ Shikieki's House ]]
"The power of the universe is in this blade. Master using it and you can have this." - Legend of Zelda, the White Sword you can get once you have enough hearts.

[[ Thunder Tower ]]
"Gah! Humans!" - Again, Nitori's first line in Mountain of Faith.
"*Ooops!* This was a Wizardry joke." - That was a Wizardry joke.
"Looks like Team Reimu's destroyed the generator agaaain! ...No, that doesn't work." - Looks like Team Rocket's blasting off agaaain!
""Rip 'n' tear 'em a new one! Have atchoo!", she's saying." - The New Udon/Tewi relationship is that of Fassad/the interpreter's in Mother 3. "Rip and tear!" is from the Doom comic.

[[ Mugenkan - Table ]]
"This seems shockingly serious." "It is quite the affair, yes." - Man, I did this even more than I remember.
"You heard her! If we're too slow, we'll all disappear!!" - Originally "Destroyed!!" (yes, in English), but I figured it was more dramatic to use the name of the final boss music.
"W-Why's that? It's not just because the engine isn't designed for more than four people, is it?" - It really isn't. RPG Maker is annoying to make stuff like this in.

[[ Outside Kourindou ]]
"Yuu-Gi: Oh. Reimu." - Yu-Gi-Oh. And once again, a general "and all those to come."
"Screw the laws of physics, I have sake." - Yu-Gi-Oh The Abridged Series: "Screw the rules, I have money!" + "Her sake not even drop."
"Then it's a D-D-D-DUEL!" - I wonder.
Yuu-Gi-Oni - Overlap from Yu-Gi-Oh mixed with Yuugi's theme, Flower-Studded Sake Dish.
"Ya-ya-YAHOOOOOOOOOO!" "Whoa, her backwards-long-jump not even stop." - Super Mario 64 TASes. And more sake-balancing skills.

[[ Palace of Earth Spirits ]]
"(I'm not an enemy. I'm a friendly mole.)" - Tutorial moles in Earthbound.
"I'm Ruffini the Dog." "Is that game designer actually still alive?" "Nah, he's dead, ze." - Ruffini the Dog from Earthbound, who was possessed by the spirit of the game designer.
"Aren't you eating? Aren't you eating?" - Tanetane Island hallucination in Mother 3.
"Ukikiki, popipo. (I'm a shop monkey.)" - Popipo, a Hatsune Miku song.
"Y-Y-Y-Y-Y-Yo-shi!" - In Japanese, "detteiu"; the sound of getting on Yoshi in Super Mario World.
"Sparky" - One of the Don't Care names for Ness's dog in Earthbound. (In the Japanese version, the corresponding name was "Masahirorin," a member of the Japanese band SMAP.)

[[ F-F-Fire Springs ]]
"The corpse trash can, F-F-Fire Springs. Was there a name like that in the original games? I forget." - Yep: Fire Spring from Earthbound, and the Mother 3 song "It's a F-F-Fire!"
"Ready, Reimu? Listen well. Or just mash the Z key, whatever floats your boat. If you've heard this speech in the original, you may NOT need to take notes." - Rock's speech in Earthbound.
"You finally got here. This is the seventh of his melodies. But it's mine now. Take it from me, if you dare..." - Your Sanctuary from Earthbound again, but even more direct than Youmu way back when.
"Congratulations! Your SPARKY evolved into DIAMOND SPARKY!" - Pokemon evolution. Although the event is in reference to what Carbon Dog does in Earthbound.

[[ Hinanai Tower - Torture Room ]]
"(Psst. Mash the Z key to restore life. If it goes down to zero, it's game over!)" - The whole torture minigame is a reference to the ones that tend to show up in Metal Gear Solid games.

[[ Hinanai Tower ]]
"I'm jes passin' through... I'm the yakitori girl!" - The beginning of the mecha scenario in Live-A-Live. The second line's actually different in her Touhou-A-Live scenario, ironically.
"...Sweethearts, you might be thinking?" - Beginning of LAL's cowboy chapter/TAL's Hourai Chapter: "Almost feels like we're sweethearts or something, y'know?" The latter references the former. Yeesh!
Theme of Moriya Warrior Sanae Kotian - Sanae's theme, Faith is for the Transient People, mixed with Theme of Space Warrior Samus Aran from Super Metroid.

[[ Yasakaya - Kanako's Office ]]
Windsong - Not sure what it's supposedly mixed with, but it's Moonsong from Cave Story with extra chimes.
"Now, kill me! Or I... shall kill YOU!" - Ballos from Cave Story.
Ancient Battlefield Showdown ~ Suwa Last Battle - Kanako's theme, Suwa Foughten Field, mixed with Last Battle from Cave Story.
"Kanako Yasaka threw a Wiimote Missile!" - Keep your wriststrap on, Kanako! She really IS an old lady.
"Kanako Yasaka charged, saying "I wanna get Miss Sanae in the butt!"" - No comment.
"Kanako Yasaka attacked with miracle fruit! In the EYE!" - One of Sanae's spellcards in Subterranean Animism Extra is "Miracle Fruit."
Suwako teleports in after the battle - JUST AS PLANNED. (That's EXACTLY what it looks like, seriously. There was even Japanese fanart with her standing there with "keikaku toori" written above her!)

[[ Underground Beach? ]]
Reimu and Marisa's dance - The Falling Love scene from Mother 1.
R-IN - The robot who interrupted said scene, but styled after Orin.
"Ah, the days of my youth..." - Marvin Grossberg from Phoenix Wright.

[[ Palace of Earth Spirits ]]
"Got the Power Glove." - It's so bad.
"Everyone got a Satori Lunchbox." - The Japanese name of the Brain Food Lunch from Earthbound, because "satori" is a state of enlightenment. I know, right?

[[ Scarlet Devil Mansion - Flandre's Room ]]
"Gah! Humans!" - Well, you can't say S didn't reuse the same thing, either.
"Got the Sneaking Suit." "Nice, black and white armor. What a suitable suit." "It's a new model of Sneaking Suit. It's designed to let you take four missiles to the face and be okay." - Metal Gear Solid.
"Magic Ribbon leveled up into MAGIC Ribbon!" - Uses the Dragon Quest level up fanfare.

[[ Hinanai Tower - Floor 1 ]]
"I'm not an enemy. I'm just a friendly fat guy." - Again, tutorial moles from Earthbound.

[[ Hinanai Tower - Keine ]]
"Be careful! Immortal people don't die when they are killed!" - People die when they are killed. But she wouldn't die even if you killed her!
"[Low Kick] [Gutsy Kick]" - Akira's attacks from Live-A-Live. She only inherited the former in Touhou-A-Live.

[[ Hinanai Tower - Eirin ]]
"...inPUT your COMMAND." - Phase Distorter in the Cave of the Past in Earthbound.

[[ Hinanai Tower - Floor 3 ]]
"Jya-jyaaan!" - Orin's first line in Subterranean Animism after turning from a cat into a cat, also inferiorly known as "tadaaa!"

[[ Hinanai Tower - a ]]
Pre-battle, battle, and post-battle music, and recovery sound - All RPG Maker RTP songs/sounds.
"a chanted Nuclear III!" "a chanted Fire III!" "Got the Dragon Sword." - Default spells and weapons in RPG Maker, naturally.

[[ Hinanai Tower - Tenshi's New Office ]]
"Received the Insignificant Object. Threw it away." - Useless item in Earthbound.
Yukari vs. Tenshi - Same as when it was just a still image in Remilia's slideshow, old Fire Emblem battle HUD.

[[ Hinanai Tower - Rooftop ]]
Porky's Porkies - Remix of the track of the same name from Mother 3, from the Porky-bots fight.
"S-IN rained hairspray from the heavens!" - Lavos from Chrono Trigger: "Destruction rains from the heavens!"
"S-IN fired its End of the Century Beam!" - Natural Killer Cyborg's ultimate attack in Mother 3.

[[ Scarlet Devil Mansion - Flandre's Room ]]
Crystal Spear: "Mankind's first weapon." - The first weapon in Terranigma, which gives you a speech about mankind's use of weapons before you can take it.

[[ Magicant ]]
"So I guess this makes me a "Flying Mima"?" - Flying Man in Magicant.
"Ufufufufufu." - PC-98 Marisa's characteristic laugh. Touhou Wiki translated it as "Mhm, mhm, hmhmhmhmhmhm" or something. Uh, sure.
"Take a melody, simple as can be." "Give it some words and sweet harmony." "Raise your voices, all day long now, love grows strong now. Take a melody of love." - Mother 1 Eight Melodies lyrics.
"Beyond here is the "Sea of Eden."" ... "Inside your mind, there is anxiety, fear, tension, unrest, and impatience." - Almost direct quotes from the Star Master in Earthbound Magicant.

[[ Magicant - Onett ]
"Like a great tapestry, vertical and horizontal threads have met..." - The second coffee break in Earthbound.
"That song was originally just a simple song from a textbook." - Eight Melodies DID end up in a music textbook. (Er, after Mother 1 created it, presumably.)
"Ness used the Made-You-Look! W-What?! I can't believe Reimu fell for that!" - Item from Mother 3 that turns an enemy around.
"Ness read the Overcoming Shyness book!" - Book to cure the Tenda of their shyness in Earthbound.
"Ness sprinkled Dragonite on his body!" - Bag of Dragonite from Earthbound.
"Ness threw a Super Bomb!" - Jeff attack item from Earthbound.
"Ness read the Moonside Press! Mani Mani is always Mani Mani at Mani Mani with all Mani Mani Mani." - Newspaper in the Moonside hotel.
"Ness read a riddle card! Reimu answered "SAKE!"" - Riddle cards from Mother 3.
"Ness sprayed Rust Promoter DX!" - Stops mechanical enemies in Earthbound.
"Ness used the Trout-Flavored Yogurt Machine! Trout-flavored yogurt was produced at the speed of light!" - Trout Yogurt Machine in Earthbound.
"Ness threw Fly Honey! Stinky!" - Belch's favorite food in Earthbound.
"Ness threw Clumsy Robot! Ping! Clankety... Rattle, rattle dwourrrrr!... Squeeeek, tweet tweet... CLANK!!" - Boss in the Monotoli Building in Earthbound, and his pre-battle... speech.
"Ness used the Casey Yoyo!" - Doesn't exist in Earthbound, but the Casey Bat does, which has a terrible chance of hitting and does lots of damage.
"I came rushing, quick! To take a photo, quick! I'm a photographic genius, that I am!" - The Earthbound photographer, one last time.
"...May the goddess of fate smile upon you." - Again, last line of Mother 2 coffee break, changed in Earthbound.

[[ Scarlet Devil Mansion - Flandre's Room ]]
"Reimu...! Thank bullets!" - Inspired by Kaguya's "Holy bullets!" from the end of Imperishable Night. Whoever did that translation is still great, by the way.

[[ Garden of the Sun ]]
"Your life, and the lives of all who believe in you... Will you put it all on the line..." - The line prior to pulling the last needle in Mother 3...
"...and board the R-EFRIGERATOR-99 (LAST DANCER)?" - ...and the last ship in R-Type Final.

[[ Main Deck of the Pizzahead ]]
Nearly every Porky/Tenshi/Rinbokusan line - Almost exactly copied from Revenge of Meta Knight in Kirby Super Star.
Touhou Mecheye - Not sure what exactly it's mixed with, but based on Main Deck of the Halberd, which played on Mecheye.
"Heavy Kisume" - As part of the aforementioned, Heavy Lobster.

[[ Skies Above Gensokyo ]]
"Now, let's go! Reimu! Don't you dare fall, or it's GAME SET, okay?!" - Falling off the screen kills you in Super Smash Bros.
"Maidens are GOOOOAAAAARGH!" - Elite Beat Agents, "Agents are GO!"

[[ Main Deck of the Pizzahead ]]
"KA-75" - 75 can be read "na-ko" in Japanese. Yep.
"Here's a final present from Sanae Kotian. I'll stop it from moving!" - Metal Gear Solid: "Here's a final present from Deepthroat. I'll stop [Metal Gear] from moving!"
Alicemoon - Based on Taking Over the Halberd, which also played on Halfmoon, (barely) mixed with The Grimoire of Alice.
Taking the Gravity Suit from Sanae - Supposedly based on being able to take a cloak from a dead sailor in Tales of Destiny.
Alex - Default RPG Maker hero. (In the beta, he also notified you that you were at the end of it after the Yuyuko/Komachi/Shikieiki cutscene.)

[[ Pizzahead - Proto-NKC ]]
"Welcome to my castle!" - Possibly the No More Heroes Rank 1 intro, as this line was in English originally.

[[ Pizzahead - Pork Eater ]]
Metal Gear Solid 3: SNAAAAAKE EATER. But really, probably the corridor with the same music in Mother 3, except I think this one is even longer given the inability to run.

[[ Pizzahead - Cave of the Past ]]
"*hop* *teardrop*" - Same as the final save frog in Mother 3.

[[ Pizzahead - Porky's Office ]]
"KNOCK OUT" - End of a match in Scarlet Weather Rhapsody.
"Yes! Reimu! Marisa! You will be just another meal to this machine..." - Porky before Giygas in Earthbound: "And you... you will be... just another meal to him!"

Disappear!! - First of all, "Disappear!!" (technically, "Inakunarinasai") is just the popular Japanese name for the original Mother 2 song, like how the English one is "Pokey Means Business."
And here's all the songs mixed into it:
Pokey Means Business (Earthbound)
Two-Colored Lotus Butterfly ~ Red and White (Dolls in Pseudo Paradise)
Dance of Witches (Immaterial and Missing Power)
Angel's Legend (Highly Responsive to Prayers)
Gensokyo, Past and Present ~ Flower Land (Phantasmagoria of Flower View)
Vessel of Stars ~ Casket of Star (Lotus Land Story)
Faint Dream ~ Inanimate Dream (Lotus Land Story)
Complete Darkness (Story of Eastern Wonderland)
Eternal Shrine Maiden (Highly Responsive to Prayers)

"I know you guys are claiming to be heroes." - Porky's mid-battle speeches in Earthbound. Other similar lines:
"You'll burn up like the garbage you are!"
"So, isn't this terrifying? I was terrified, too!"
"Go ahead, cry your eyes out! Isn't this just pee-your-pants scary?!"
"Reimu! It's going to seem like I'm running away, but I've merely decided not to kill you!"
"I'll just sneak away to another era to think about my next plan."

[[ Pizzahead - Cave of the Past ]]
"Guide my inner shadow... Light and dark above... And transcend the stars!" - Golbez from Final Fantasy Dissidia.
Battle Against Gensokyo - Battle Against the Masked Man from the end of Mother 3, mixed with Border of Life, the Windows Touhou title screen music, and Necrofantasia.
"Mima jumped in front! Mima took 9822 mortal damage! Mima fell to the ground." - One last, most appropriate time, Flint's sacrifice in Mother 3.

[[ Cast Roll ]]
"STUFF" - Typo in the Death Crimson credits.

[[ Yuka's Smashes ]]
Yuka: Aether! HYAAAH!
WE LIKE IKE!!

Marisa: Where'd you get that hammer?!
FROM HAMMERSPACE!!

Yuka: Enough is enough! I've had it with these fairies!
SAMUEL L. JACKSON!!

Yuka: Henshin-a-go-go, ladies!
VIEWTIFUL JOE!!

Yuka: Just take a look at THIS!
RESIDENT EVIL!!

Yuka put down her weapon for a bare-handed strike!
Yuka: FAL-CON! PAUUUUUUUUUUNCH!
CAPTAIN FALCON!!
Yuka: Show me your moves!

Yuka: There's... no one inside you, is there...?
SCHOOL DAYS FINALE!!

Yuka: When you don't go to heaven, tell 'em little miss Yuka sent you!
DEPARTMENT STORE SPOOK!!

Yuka pointed her fingers at the enemy!
Yuka: Bang!
THESE ARE METAL GEAR SOLID 4: THE GUNS OF THE PATRIOTS!!

[[ Mima's Smash ]]
?! ...What did Miss Mima do?!
PORKY IN MOTHER 3!!

[[ Miscellaneous Items ]]
ATM Card: "Withdraw money! Take that, Ribbity!" - In Mother 3, the save frogs managed your money rather than Earthbound's ATM machines.
Maxim Tomato - Kirby item that refills lots of health (or all, in some cases).
Mani Katti - One of Lyn's weapons in Fire Emblem 7.
Suporma - Orange Kid's greatest invention, only created if you choose to fund him in Earthbound. It sings an Ode to Orange Kid and promptly breaks.
Giggle Charm - ""Ugigi" is written on it. Ugigi." - Yuugi's characteristic laugh. But Touhou Wiki translated it as "Geez!" Geez!
Elfire, Fimbul - Fire Emblem spells.
Monster Trap - Monster Hunter.
Rollin' 21, 27, 29 - Issues of... THAT kind of Touhou doujin. I was informed of this by someone else. Blame them.
Game Boy (as a shield) - Well, it IS made of Nintendium.
Gutsy Glove: "Passin' through; it's equipment, guy!" - Equipment from Live-A-Live, and yet another parody of the "I'm the taiyaki guy!" line.
Infinite Bandana - Snake from Metal Gear Solid has a bandana that gives him infinite ammo. Somehow.
Ohm Cane - Item from Fire Emblem 1, though apparently it was actually the Ohm Staff. Too lazy to change it, honestly.
Story of Dedede in Dreamland - A long-running Kirby manga.
Melio Scutum - Glyph in Castlevania: Order of Ecclesia.

[[ Battle Memory ]]
Cirno
"Enemy or friend?" - Mole Cricket's Battle Memory description in Mother 3.

Mr. Ghosty - I don't think the PC-98 ghosts ever had an official name, so they're named after Mr. Batty from every Mother game.

Starman Jr.
"A young spacenoid" - Once again, the Cho Marisa page is the best.

Undefined Border Occupier - Touhou 12 revealed that the Touhou term for UFOs is apparently "Undefined Fantastic Object," so I rolled with it.

Even in Your Mother Game - IOSYS's FOE video: "Even in a boss fight, FOE!" and so on.
"Don't look this way." - "Kocchi minna," the 2ch name for the face given to FOEs.

Gramps Rider
"All his friends know him. He's a little taller than most coots his age, but he takes it easy down the stairs of Hakugyokurou." - Low Rider.

Spiderman!!!!!! - Gee I wonder.
"Your friendly neighborhood spider from hell." - Spiderman, Spiderman, friendly neighborhood Spiderman.
"To tackle him calls for great power and decent agility." - Or great responsibility, but if that were the case Yuka might actually be eligible.

Half-Spirit - Youmu is half-human, half-ghost, and half-baked.

Youmu Shall Not Lose
"But I know something you don't know. I... am not ambidextrous." - The Princess Bride: "But I know something you don't know. I... am not left handed."

Poopachu - Pikachu gone wrong.
"He strives to be the very best!" - English Pokemon theme song. Also, Pokemon games sorta like exclamation marks.

Wriggle
"Pretty good for a bug." - One of the drama tracks about Wriggle on IOSYS's Anthology of Ice and Snow.

Usagator - "Usagi," rabbit, plus gator.
"An alligator that might be a rabbit, or a rabbit that might be a plate of sashimi." - Zeal-ian in Chrono Trigger: "Am I butterfly dreaming I'm a man? Or a bowling ball dreaming I'm a plate of sashimi?"

Starman EX
"An extra stage Starman. If you were wondering who an unknown Starman was, it was probably him." - U.N. Owen Was Her?

That Rascally Rabbit - Be wery, wery quiet. I'm huntin' wabbits.
"Their stupid maze tricks are for kids." - Silly rabbit! Trix are for kids!

Spinnnnnnnnnner
"Can reach around 85 centimeters on a good day." - The Megurine Luka song Double Lariat: "The radius of 85 centimeters, it's the distance I can reach around."

Cirno
"Nine balls stand on the edge of a cliff. They all fall off. Cirno thinks the same way." - Zybourne Clock: "Four balls stand on the edge of a cliff." ... "Time works the same way."

Eyes On Byu - Eyes on You from Final Fantasy VIII. Somewhat unintentionally.

Elly
"Is it lonely? Is it sad? Though she's had plenty of time to think about it, she says she doesn't know." - Bad Apple!!

Severed Head
"Reimu had a dream. It was a very clear and very strange dream, starring a headless prince." - Before the Poo segment in Earthbound: "Ness had a dream. It was a very clear, and very strange, dream."

Huoooh! - Balrog's exclamation as he saves Quote and Curly from Hell with the power of his head.
"A lunchbox... What? You mean that's just the door behind him?" - People call Balrog from Cave Story a lunchbox because it looks like he has a handle the first time, but it's actually just a door.
"You don't say." - I do say. (Curly from the best ending after beating Ballos.)

Only God
"A legendary Fire-type; a half-dog, half-gerbil creature seen by few." - Pokemon Gold/Silver/Crystal introduced the three Legendary Gerbils: Entei, Raikou, and Suicune.

I, Demon - I, Robot.
"What was his creator doing to necessitate this?" - He's from Holy Invasion of Privacy, Badman! What Did I Do to Deserve This? (AKA What Did I Do To Deserve This, My Lord?!)

Lady Shinki
"That stray hair strand of hers is capable of piercing the heavens." - Gurren Lagann, drill that will pierce the heavens, etc.

Natuve Faith - The Pokemon Natu (even though it's more like the evolution, Xatu) plus Suwako's theme.
"Holy bullets!" - Kaguya from the end of Imperishable Night.

Cirno
"Some wrestler guy with equally-low IQ, I think." - Masaru from Live-A-Live has a maximum IQ of only 25, even with the best equipment. Also, Cirno meets him at the end of her Touhou-A-Live scenario.

Bunnymask
"Who could be wearing that mask? ...A Hylian?" - Bunny Mask from Ocarina of Time and Majora's Mask.

Godmask
"A Pigmask with deadly weapons on both arms, not just his right." - Gene's right arm is the God Hand, though he does get the Devil Hand on his left for the final battle.

Uncyclopedia - Yes, there's a Japanese version of Uncyclopedia. It has an equivalent to the AAAAAAAA article, too.

Count Remilia
"The embodiment of charisma." - Remilia is the titular Embodiment of Scarlet Devil.
"Despises Rinnosuke for being a miserable little pile of secrets." - What is a man?!

Smilin'ball - Modification of Earthbound's Smilin' Sphere.
"Reimu sees his yellow half and wants it painted black." - I see a red door and I want it painted black.

MAN
"He's a man and a half." - Who's a man and a half? I'm a man and a half! (The Doom comic, but was also referenced by Rinnosuke in one of the pages of that "manservice" comic.)
"Nice muscle" - Muscle March.

Snake?! - Snake? Snake?! SNAAAAAKE!
"It's his destiny to be here." - Calling Sigint in a box in MGS3: "It's my destiny to be here... in the box."
"Border Inc." - IOSYS's Border Incorporated Company Song.

Passhon - Mr. Passion/Lord Passion from Mother 3.

Bravopig
"Exteeeeending aaaaarm" - One of Nitori's spellcards in Mountain of Faith.

Old-E - Oldie, but a goodie.
"It's not just a piece of junk; in fact, by and large, it's better than the new models." - Wall-E, and the Buy and Large company from said movie.

Pizzah
"The favorite food of devil hunters everywhere." - Dante eats pizza in the most radical way in the opening cutscene of Devil May Cry 3.

Shanghai Tease
"It loves to play danmaku..." "One coin" "No continues" - Conversation before Reimu fights Flandre.
"But only with the strict rules of one-coin, spellcards-only, no-continues." - No items, Fox only, Final Destination.

Big Bang Easy
"There's... no one under that hat, is there?" - School Days Finale, again.

Ancestral Starman
"He's bad, and everybody knows it." - You know he's bad, he's bad, you know it.

Lunastone
"Make sure you don't forget the "s."" - What, you mean "Lunatone" - OH NO COPYRIGHT INFRINGEMENT

Positiveman - The opposite of Mother 3's Negativeman.
"We're not sure what would happen if Lady Eiki ran into him." - Evidently, according to S, Shikieiki is suicidal, though if that's meant to come across in her dialogue you sure got me.

Hot, Yo!
"Feels good" - Feels good man.

Ghostcluster - Who you gonna call? Ghostbusters!

Melty Moltenman - Melty Molten Galaxy from Super Mario Galaxy. (Which was originally "Hell Prominence Galaxy," oddly.)

Cypork Ninja
"A Pigmask with a rough voice. No one in Gensokyo knows where he's from, though some say he died once." - Cyborg Ninja from Metal Gear Solid.

Wildcat - Ocelot.
"His reloading alone makes him revolutionary." - Ocelot in MGS3: "Reloading like this... it's a revolution!"

Pigmask Agent
"He lives a life of danger, chance-taking, and curry for every meal." - Secret Agent Man.

AAAA - Generic RPG hero name if you're lazy.
"A standard cocky hero that makes bad guys wonder what they did to deserve him." - A hero from Holy Invasion of Privacy, Badman! What Did I Do to Deserve This?/What Did I Do To Deserve This, My Lord?!

Cerebrum Final Mix - Cerebrums from Mother 1.
"No one has any idea what "Final Mix" is meant to imply." - Probably Kingdom Hearts Final Mix. Or should that be Kingdom Brains?

Final-E - In the finale of the finale...

Smooth Shambler
"A Shambler that's smoother than silk doing the moonwalk. Sure, he's an enemy, but attacking him seems so... criminal." - Alice, are you okay? You've been hit by... a Smooth Shambler!