ATTACK OF THE CHICKENS(ZELDA)

Starting with A Link to the Past, attack a chicken as much as you can and an entire army will get their revenge on you

METAL GEAR-VANIA

Have Castlevania Symphony of the Night on your PS1 memory card and he'll reveal the game on your memory card. This works with other Konami games including Azure Dreams, Suikoden, and Vandal Hearts. The Gamecube remake also brings this back, this time with Legend of Zelda Windwaker, Super Mario Sunshine, Super Smash Bros Melee, and Eternal Darkness

CLOUD JOINS THE PARTY(FINAL FANTASY TACTICS)

A sidequest that is activated after finding a certain Zodiac Stone, you can get Cloud from Final Fantasy Tactics to join your party, complete with most of his Limit Breaks from the game. The PSP remake of the game follows up on this by re-including Cloud, as well as Luso(FFTA2) and Balthier(FFXII)

LINK AND SAMUS IN SUPER MARIO RPG

Both Link and Samus make appearances in Super Mario RPG, sleeping in some inns before/after(respectively) facing battles with their foes

BATTLE CUTMAN(MEGAMAN X8)

If you have a save file of Megaman X Command Mission on your PS2 Memory Card, you can unlock a battle with Cut Man from Megaman 1

STARFOX REPORTING FOR YOUR MASKS

A line of masks in your inventory in Majora's Mask will appear to represent the Starfox crew+Pigma

SOMETHING'S WRONG WITH THE G-DIFFUSER

Appearing in F-Zero X, James McCloud in F-Zero is pretty much the same character from F-Zero. Since his appearance in F-Zero X, he's since become a staple

ROOM OF GABEN(HALF-LIFE)

The God among PC Gamers has his face plastered in a room in Half Life...which is kind of creepy

RESIDENT GAMECUBE(RESIDENT EVIL REMAKE)

In the Gamecube Remake of the original Resident Evil, the MO Disc Reader was changed to resemble the Gamecube(as a nod to the game's exclusivity). Unfortunately since the recent HD update of the game isn't available on any Nintendo consoles, the GC resemblance has been removed

STARTING THE CONSOLE(NINTENDO GAMECUBE)

Holding the Z Button with one Controller will make an alternate sound when starting up. Do it with all four controllers and you'll get another start up tune