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Animal Crossing is pretty much chock full of references to other Nintendo games. The one for the GameCube (i.e. the first one released outside of Japan) had a Pokémon Pikachu villagers would sometimes request from other villagers, as well as items like the previously mentioned Arwing, a Master Sword, and a hidden set of Super Mario Bros.-themed furniture. Not to mention that the game borrowed some sound effects from Super Mario Bros., like the familiar coin sound representing Bells, the game's currency. The same sound would also play when hitting rocks with money hidden in them, which would change to the 1-Up sound effect as the amount of money increased. Wild World for the DS added even more, like a Triforce and more hidden items, like a Blue Falcon, Pikmin, and a Metroid. Both games also have a blue bench with the Nintendo logo, with it being hidden in the original and being an ordinary item at Tom Nook's store in Wild World.
In a non-Nintendo-related example, a blue eagle townsperson named Pierce has the Verbal Tic"hawkeye".
All three iterations of Animal Crossing have a frog villager named Jeremiah, a reference to the Three Dog Night song "Joy to the World".
Lots of Animal Crossing characters make specific references to Zelda, for some reason. "Perky" type girls in Wild World will sometimes tell you how they traveled to a nameless "far-off land," where they met "a cute boy with green clothes and a Magic Boomerang." In the original, the sailor Gulliver talks about one of his various girlfriends, who allegedly lives in Hyrule. Hyrulian Loach, anyone?
In City Folk you can get Midna's Mask and wear it.
In Kirby's Dream Land 3, one of the level objectives is to defeat a bunch of Metroidsnote with Kirby's ice attack, naturally. Samus herself rewards you with a heart star for doing so. She even takes off her helmet for '100% completion'.
Occasionally in the SNES version of Donkey Kong Country 3, you can enter Wrinkly's Save Cave and find Wrinkly Kong playing a Nintendo 64. The music in the background when this happens is an arrangement of the music that plays inside Peach's castle in Super Mario 64.
An internal Rareware shout-out: in Donkey Kong 64, the Ghost Books found in Creepy Castle are all but identical in appearance to Cheato from the Banjo-Kazooie series (in fact, this is their Japanese name).
Mario characters are drawn on the walls on Wuhu Island in Wii Fit Plus. In the Jogging Plus game you have to remember which one you passed. The ocean liner docked off Wuhu Island? As revealed in Wii Sports Resort, it's called the Queen Peach. And in Sports Resort's Island Flyover game, there's the sound of someone in the Hill Village playing Super Mario Bros. on the NES.
The icon for the Links club in the portable Mario Golf games is a recolored Triforce. This doubles as a Stealth Pun.
One rather bizarre reference occurred in The Legend of Zelda Oracle games. In the linked game, Zelda gets kidnapped and you have to save her...by going through a side-scrolling area with lots of ladders and rolling fireballs. In other words, Link has to play Donkey Kong.
In The Legend of Zelda: Twilight Princess, there are the characters Thelma the bartender, and her cat Louise. Granted, her in-game name is Telma, but it's because Japanese doesn't really have a "th" sound. The name should be "Thelma", it was just mistranslated.
Also in Ocarina of Time, the Kokiri race has various allusions to Peter Pan, such as them being accompanied by fairies, their child-like image and playfulness, and the fact that they can't grow up. Also, Miyamoto has stated that Navi has a crush on Link and is jealous of Zelda, an allusion of Tinkerbell being in love with the eponymous main character and being jealous of Wendy (coincidentially, this kind of relationship was also in the Western animated series).
The Bremen Mask in Majora's Mask is named after a Grimm's Fairy Tale titled Town Musicians of Bremen, in which a group of animals (a donkey, a dog, a cat and a rooster) decide to leave their masters and become traveling musicians. In the game, the mask can be used to make chicken march behind you.
It's confirmed by the longtime developers of the Zelda series that the trading sequences present in several games are inspired by Straw Millionaire, a Japanese Buddhist folk tale.
The Ancient Cistern has a design and concept that has been closely compared to the events of the Japanese story The Spider's Thread.
Koji Kitagawa, one of the developers of Skyward Sword, said in an Iwata Asks interview that the Ancient Robots were modeled after the Dogu clay figurines, a commonplace treasure from the Jomon period of Japan.
The way that Link swings his sword around the eye in Skyview Temple to make it dizzy is similar to how you defeat Mr. I in Super Mario 64.
In the lead up to the fight with Tentalus, Link has to get to the top of the ship, up a series of ramps, with barrels coming down the other way. It's a nice callback to Nintendo's early history.
When Link initially meets Thunder Dragon, he thinks his name is boring and due to hanging out with robots too long, half-jokingly wants to call him LD-Link-16. Fittingly enough, if you count Oracle Of Ages and Oracle Of Seasons as two seperate games, this Link is indeed the 16th.
Starbeans Cafe is a play on Starbucks, obviously. Olimar (who dubs Mario "Marlio") and his Pikmin, Samus, Link, Wario (who calls himself a guest star), Fox, Peppy and Slippy, and even an Excitebike racer were planned to appear and give the Mario Bros. useful items. The items were still used in-game, but the names were changed.
The game features an in-game storybook with an art style noticeably similar to the illustrations from The Little Prince. Many people had commented on how Super Mario Galaxy was oddly reminiscent of the book before its release.
There's also a small mechanical planetoid in the Buoy Base Galaxy that looks like a Pokeball. Also, at some point during the Space Junk Galaxy, Mario lands on Olimar's ship.
The Warp Whistle item plays the same musical notes as the Recorder in The Legend of Zelda, and it also summons a tornado that carries the player character elsewhere the same as the Recorder does. A redone version of the tune can be heard on the title screen of The Legend of Zelda: Ocarina of Time.
In the English version only, at the end of the game, Princess Peach says, "Thank you. But our Princess is in another castle!...Just kidding! Ha ha ha! Bye bye." This refers to "Thank you Mario! But our princess is in another castle!" from the original Super Mario Bros..
Super Mario RPG has the Pipe Vault area, a one-block-wide underground area reminiscent of Super Mario Bros.' underground stages, complete with their music and pipes containing Piranha Plants. And then there's the curtained alcove in Booster Tower, where Mario will transform into his eight-bit self for a few seconds. In addition, there are a couple of easy-to-miss cameos made by Link and Samus.
The game also has references to several Final Fantasy elements, considering Squaresoft helped make the game. Culex, a Bonus Boss, has a battle theme, victory theme, and prelude all in the style of Final Fantasy IV.
The game also has a less obvious shout-out to Final Fantasy in the form of one late-game boss; the Czar Dragon and its undead counterpart Zombone. They take their names from two enemies from Final Fantasy VI, although the former was Dummied Out.
Super Paper Mario takes it a step further- whenever a character grabs a star, they turn into a giant 8-bit version of themselves that rampages across the screen. Inversely, another powerup gives you a small team of 8-bit versions of yourself that surround you and help defeat enemies, though they rarely last long. Also, the Underchomp battle plays like a Dragon Quest battle (but may also be a reference to EarthBound), the Pits of 100 Trials resemble a Game & Watch display, and the Mansion Patrol minigame is a fairly obvious reference to Luigis Mansion. And Mimi and her Transformation Sequences appear to be shout-outs to both The Exorcist and The Thing (1982).
Metroid has multiple references to the Alien series of films. Most obviously, the recurring boss Ridley, who shares a name with Ridley Scott, director of the original Alien and the Metroid egg seen at the end of Metroid 2 and the start of Super Metroid uncannily resembles a facehugger egg sac.
The Star Fox series seems to have a number of reciprocal Shout Outs in relation to F-Zero. For starters, Fox McCloud and Falco Lombardi may have originally been Shout Outs, being an anthropomorphic Golden Fox and Blue Falcon respectively. Then, James McCloud (outfit and all, but in non-anthropomorphic human form) became a character in the F-Zero series starting with F-Zero X. Then Star Fox Command references F-Zero yet again, where one of its nine possible Multiple Endings has Fox and Falco becoming racers in a high-speed racing league called G-Zero.
Even the anime F-Zero The Legend of Falcon has O'Donnell being referenced as James's deceased friend.
General Pepper not only owes his name, but also his very outfit, to the landmark album by The Beatles; Sergeant Pepper's Lonely Heart's Club Band.
Captain Shears, a character from "Farewell, Beloved Falco", is similar in both physical appearance and attire to Pepper and appears to have a name derived from "Billy Shears", the fictitious leader of Sgt. Pepper's Lonely Hearts Club Band.
In Farewell, Beloved Falco, one of the Hot Rodders (Falco and Katt's old gang) is Mouser — Mouser's name is even on the back of his jacket.
In Assault, there are classic Namco arcade references and cameos littered in the game, one being the yellow S flag from Rally X; after all, Namco did develop this game.
In Star Fox 64, shortly after you enter Meteo's Warp Zone, you'll be treated to several waves of bee/butterfly-like enemies that fly in formations very reminiscent of Galaga. You get bonuses if you can nail them all.
Star Fox 64 has Katina, which is pretty much the climax scene from Independence Day, complete with Bill Gray, a nod to Gen. William Grey, Robert Loggia's character in the movie.
The character Mr. Sandman is a tribute to some Real Life boxers: Joe Frazier in the arcade, NES and SNES games, Muhammad Ali in the Wii version, and Mike Tyson in the Wii game as well, but in Title Defense mode.
During an intermission after a round in the fight against the Bonus Boss of the Wii game, Donkey Kong, Doc Louis jokingly tells Mac that he (Louis) can call his plumber if he (Mac) is having problems. This is a reference to Mario, who was a plumber and used to antagonize with Donkey Kong in the past.