Xbox360 for sure. It's the right size for my hands, is comfortable, all the buttons are in the right place for my fingers, said buttons are easy to press and my thumbs never slip off the thumb-sticks. I don't get why people have such negative opinions about the D-Pad, though. It's a D-Pad and it works as such, I've never had any problems with it and I don't understand why people have such gripes about it :l.
The Gamecube controller is probably the most comfortable controller I've ever used. But it's a bit small for my hands, the C-Stick and D-Pad are pretty stuffty and I always found that my thumb would slip off the thumb-stick easily.
I really don't like PlayStation controllers in general. The buttons, thumb-sticks and D-pad are all fine but the controller just feels too small and I just don't find the shape comfortable at all :/.
I don't remember enough about my experience with the N64 controller to have much of an opinion but I do remember that I found it quite awkward to use.