Metroid & Shinobi
Pit & Sonic
Kid Icarus (Pit) & Marth
Sakura Samurai & Shinobi
Dillon & Sonic (perfect for each other, no homo. LOL)
Metroid & Halo
Ketzal's Corridor & Pushmo and/or Crashmo
Kid Icarus & World Ends with You
Kid Icarus & Kingdom Hearts & Final Fantasy
Zelda & Shinobi
Zelda & Sakura
Dark Pit & Shadow the Hedgehog
Mario Kart 7 & Sonic and All Stars Racing Transformed
Luigi's Mansion & Beyond the Labyrinth
Spirit Camera & Beyond the Labyrinth
Zelda & King of Pirates
Kid Icarus: Uprising & Rodea the Sky Soldier (ultimate crossover)
Metroid & Mega Man
I might come back to edit in some more.
EDIT:
F-Zero & Extreme G
Mario Kart & Extreme G
F-Zero & Spy Hunter
Paper Mario & TheatRhythm Final Fantasy
Kid Icarus & Rhythm Thief
Star Fox & BattleTanx & Vigilante 8
F-Zero & Hydro Thunder
Smash Bros. & Power Stone
Pokémon & King of Pirates
Pikmin & Pokémon Mystery Dugeon
