NES: Super Mario Bros. 3
SNES: Super Mario World
N64: Super Mario 64
GBC: Pokémon Crystal
GBA: Super Mario Bros. 3
GC: Melee
DS: Mario Kart DS, New Super Mario Bros., Pokémon Diamond (tied!)
Wii: Super Smash Bros. Brawl, Super Mario Galaxy (tied!)
overall: Brawl and Galaxy!
I know I put too many games but I wanted to do one (or more!) for each system.