Super Mario 64.
If we're doing one per console it'd have to go like this:
NES - Super Mario Bros. 3
SNES - The Legend of Zelda: A Link to the Past
N64 - Super Mario 64
GC - The Legend of Zelda: Wind Waker (I like Twilight Princess even more but never played it on GC)
Wii - Super Smash Bros. Brawl