Donkey Kong 64

In the third area of Donkey Kong 64 (Frantic Factory), there sits a classic Donkey Kong arcade unit. As DK, you can play this game for two banana coins. Beat it, and you'll recieve a golden banana, and later on the Nintendo coin.

Legend of Zelda: Majora's Mask

Mario makes yet another Zelda cameo. This time, he appears as a mask on the mask salesman's backpack, along with a Darth Maul and Elvis mask.
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The Mask

Just like in Ocarina of Time, there are characters who wear Bowser medallions. This time, they are found at Romani Ranch.
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The Bowser Medallion

Legend of Zelda: Ocarina of Time

In the courtyard of Hyrule Castle, where you meet Zelda, there are windows on the left and right walls. If you look inside the windows, you can see portraits of Yoshi, Peach, Mario, Bowser, and Luigi.
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Yoshi, Peach, and Mario
-Bowser and Luigi

At Lonlon Ranch, Malon, Talon, and Ingo all wear Bowser medallions through the course of the game. Interestingly, Talon and Ingo were intended to look like Mario and Luigi by Shigeru Miyamoto.
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Talon and the Bowser Medallion

Mario Golf

In tournament mode, you can view a list of competitors between holes while checking your rank. Many of the names here are taken from Mario games. Some were also taken from Star Fox 64 and Legend of Zelda: Ocarina of Time, including (but not limited to) Fox, Falco, Slippy, Peppy, Link, Zelda, Shiek, Impa, Nabooru, Rauru, Saria, Ruto, Darunia, and Gannondorf.

Pilotwings 64

In the "Little States" stage, on Mount Rushmore, Mario's face has taken the place of George Washington's. While playing the cannonball game, if you collide with Mario's face, it will turn into Wario.

Pokemon Stadium 2

In Pokemon Crystal, Gold, and Silver, you can collect classic Nintendo consoles to put in your room, including a NES, Super NES, Virtual Boy, and N64. If you upload data from one of these games onto Pokemon Stadium 2, you can view these consoles in 3-D. Turn one on, and you can see a scene from an actual game that was released on the system.
The NES games include Super Mario Bros., Donkey Kong, Legend of Zelda, and Kirby's Adventure.
The Super NES selection includes Super Mario World, Legend of Zelda: A Link to the Past, Kirby Super Star, and F-Zero.
And the N64 has scenes from Super Mario 64, Legend of Zelda: Ocarina of Time, Star Fox 64, and Wave Race 64.

Super Mario 64

After collecting all 120 stars, the grate outside of the castle will open to reveal a cannon. Grab a wingcap, jump in, and blast Mario onto the roof of the castle. There, Yoshi is walking around. Talk to him, and he will thank you for playing the game, give you 100 lives. Afterward, he jumps off the roof into the distance. The only way to see him again is to start a new game.