Wiimote + nunchuck is the best.
As far as more traditional controllers go, Gamecube's is the best. I still prefer it for certain kinds of games like Smash Bros. I really like the way the buttons are laid out. With the big A button in the middle there's no question what the main action button will be, and with the different shapes and sizes of buttons it's so easy to know which one your thumb is on by feel alone.







