The Nintendo Wars game Advance Wars: Dual Strike introduced tag powers, a few of which were named after songs and musicians. For instance, Jake and Rachel get "Orange Crush" for theirs, Olaf and Grit get "Snow Patrol", while Lash and Hawke get the decidedly cheeky "Rebel Yell".
Animal Crossing is chock full of references to other Nintendo games.
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 have a frog villager named Jeremiah, a reference to the Three Dog Night song "Joy to the World".
Lots of 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'.
Cat-o'-9-Tails is possibly one: it looks similar to a hedgehog (especially since its tails are easy to mistake for spines unless you really look at it), and has a color palette suspiciously like Sonic the Hedgehog's.
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).
One nearly nobody outside of Japan would know: The Legend of Zelda: Ocarina of Time and The Legend of Zelda: Oracle Games feature two elderly witches named Koume and Kotake. The extremely influential Japanese mystery novel The Village of Eight Graves also features twins named Koume and Kotake. Both sets are identical Creepy Twins who are treated like a single character and are responsible for raising a man who isn't their birth child, who they continue to support even after he grows into an evil tyrant.
The Legend of Zelda: Spirit Tracks, according to Eiji Aonuma, was inspired by Japanese children story The Tracks Go On, a tale he once read to his son.
Zelda games often contain numerous shoutouts to each other, for example, in Majora's Mask, the various members of the Indigo-Gos are playing musical themes from The Legend of Zelda and The Legend of Zelda: A Link to the Past in their rooms.
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, dogs, and the Ikana royal guard 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 Loftwings were modeled after shoebill birds. Also, Link's Loftwing shares the colors of the Dyna Blade.
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.
When the brothers are asked to escort Princess Peach through Teehee Valley, she asks, "Won't you take me to...Little Fungitown?", a reference to the 1980 song "Funkytown" by Lipps, Inc.
In Yoshi Theater, you can see a poster with Kirby on it that says, "Kirby Story". Other posters include The Legendary Starfy and WarioWare.
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. Although the Video Game Remake didn't revive this concept, it does make the Great Force/Triforce connection even more explicit—it was redesigned slightly to more closely resemble the Triforce's appearance from Ocarina of Time on, and it even plays the series' "item get" fanfare when you obtain it.
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.
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..
Mario Party 2: When you pass by the milk bar in Western Land, you have the option of inviting the other players to a hootenanny (with the potential of setting them back from getting a star before you can). If you refuse, the Wiggler running the bar will say "Y'all come back now, y'hear?"
Mario Party 10: One minigame is titled "Fruit of the Doom", which is a reference to the American clothing company Fruit of the Loom.
Mario Party: Star Rush: One of the Coin Chaos minigames is called Steal Diver, and it has the players control a submarine to collect coins. The name is a reference to the Steel Diver series of 3DS games, which also involved submarines.
The game has a shout out towards a lives count glitch that appeared in Super Mario Bros.. If your lives exceed 999, your lives count reads as a crown and a random symbol. There's also a Brutal Bonus Level in Special World 8, which is dubbed World 8-Crown.
In a level set inside a pyramid, one of the side rooms is empty apart from a torch in each corner. If you light all of these with Fire Mario, the 'Puzzle Solved' jingle from Zelda plays and a collectable appears.
The game 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 has references to several Final Fantasy elements, considering Squaresoft helped make the game. Culex, a Superboss, has a battle theme, victory theme, and prelude all in the style of Final Fantasy IV.
The game 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 Luigi's 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 II: Return of Samus 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 F-Zero: GP Legend 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 the climax scene from Independence Day, complete with Bill Gray, a nod to Gen. William Grey, Robert Loggia's character in the movie.
The boss of sector X says "where is the creator?", and in its death throes, says "I must be complete." A reference to V'ger from Star Trek: The Motion Picture.
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 an Optional 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.
9-Volt and 18-Volt's stages in the WarioWare series have many references to old Nintendo games, including some obscure ones like Mario Clash for the Virtual Boy.
Ring Fit Adventure has World 14, which is an homage to Silent Hill. It's shrouded in a thick fog and one NPC even mirrors Harry's famous line "Have you seen a little girl..?" in reference to her own missing daughter.
Both promotional material and an Easter Egg hidden in one of the Hero Mode stages compare the Inklings and Octarians to Bloopers and Octoroks, respectively. A Blooper also appears on a poster in the Urchin Underpass stage, and an 8-bit Octorok poster appears near a chain fence. A more obscure Mario enemy, the Gunion octopus from Super Mario Land, can be spotted in certain areas as well.
The N-ZAP 85 and 89 weapons are NES Zappers; they're colored grey and orange, respectively, referencing how the Zapper was recolored orange in 1989 as an effort to make it less realistic. Sheldon mentions that the latter weapon was changed to orange for "legal reasons".
The Booyah Bomb is a clear reference to the Spirit Bomb, in both visual performance and actual function.
In one of the Octo Expansion stages, which revolves around switches that temporarily stop time, Pearl at one point quips "Time, I command you to stop!"
, a Japanese Buddhist folk tale.