Well unlike Joel, I'm not going to make a list that amounts to seeing how many poular games I can say are crap in one post for the purpose of creating some controversy .

Worst FPS: Rainbow Six (N64)
Worst RPG: Quest 64 (the worst I can think of right now)
Worst RTS: Star Wars:Empire at War
Worst Fighting: Ehrgeiz
Worst Sports: I'm going to say any fishing game, but only because fishing bores me and I don't play nearly enough sports games to be specific.
Worst Platformer: Donkey Kong 64
Worst Racing: That Mega Man racing game that appears in the Mega Man X collection.