The Gamecube controller is easily the best, with the N64 coming a close second. Nintendo has always been the best IMO in creating ergonomically designed controllers. The Gamecube is so perfectly moulded to your hands that you can sometimes forget it's there.
Control scheme is also what the Gamecube does well. All the buttons are easy to reach and, for me, it's easier to remember the controls for a new game on GC controllers. The only small problem is the L and R buttons. Sometimes, when you need to be quick, the analogue prevents you from doing so (e.g. in Smash when you need to block/dodge, although in Brawl you can reassign the buttons).
The N64 came second only because of the horribly designed control stick, which wears out easily and can hurt your thumb/palm (Mario Party
I also have a PS3, and the controllers aren't bad, but they feel very loose and they don't mould to your hands very well. Also, the control sticks have rounded edges, instead of the grooved ones on Nintendo controllers, making it harder to move in a straight line.