Firstly, this is a cool thread.
NES: Rockman 2, Runner up: Ice Climbers
Megadrive: Brian Lara Cricket, Runner up: Mario
PSOne: Metal Gear Solid, Runner up: Resident Evil 3
PS2: Quake 3, Runner up: Gran Turismo 3
Gamecube: Metroid:Prime, Runner up: Wind Waker
Xbox: Halo 2, Halo 1
Wii: Mario Galaxy, Metroid Prime 3
PS3: Metal Gear Solid 4, Demon's Souls
X360: Gears of War 3, Mass Effect 2
PC: Counter Strike 1.6, Warcraft 2