Okay, let's do this again (comparing the N64, GameCube, and Wii's software libraries). The best games on the N64 are Super Mario 64, Majora's Mask, Ocarina of Time, and Super Smash Bros., in that order. The best games on the GameCube are Resident Evil 4, Metroid Prime, Smash Bros. Melee, and The Wind Waker, in that order. The best games on the Wii are Super Mario Galaxy 2, Super Mario Galaxy, Twilight Princess, and Smash Bros. Brawl, in that order.
N64 vs. GameCube
Resident Evil 4 > Super Mario 64
Metroid Prime > Majora's Mask
Melee > Ocarina of Time
Wind Waker > Smash 64
GameCube smashes N64
N64 vs. Wii
Super Mario Galaxy 2 > Super Mario 64
Super Mario Galaxy > Majora's Mask
Twilight Princess > Ocarina of Time
Brawl > Smash 64
Wii smashes N64
GameCube vs. Wii
Super Mario Galaxy 2 > Resident Evil 4
Super Mario Galaxy > Metroid Prime
The Wind Waker > Twilight Princess
Melee > Brawl
More or less even, probably a slight victory for the Wii solely based on the cream of the crop
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Currently Playing - Resident Evil 4
Hopefully Next Up - StarCraft, Final Fantasy VII, Resident Evil 2