Use the right tool for the job.
I agree -
2-D Platformers and most classic games -> d-pad, joystick, or keyboard (my preference is joystick, but I'm an old-timer)
3-D Platformers -> modern console (except Wii)
First person shooter -> mouse and keyboard
Real time strategy -> mouse and keyboard
Flight simulator -> joystick and keyboard (unless you spring for a more involved setup)
Driving -> steering wheel and pedals.
Rhythm -> unique controllers - here the controller basically is the game, and the games are differentiated primarily by the controller.
Wii -> Motion controllers like these are still in their infancy. Wii Sports, etc., hints at what's to come.
I second another post that comments that modern console controllers (Wii, not withstanding) are jacks of all trades, masters of none. They work reasonable well for a huge gamete of game types, but I think 3-D platformer is the only game type that I think they are the best choice for.
I also think that for most games, simpler controls are better. Fewer buttons, less complicated maneuvers all allow the game to picked up quickly by a large number of people. Some people really enjoy mastering complicated controls, and that's fine. I just don't think that complicated controls make games fun for the majority of people.