Both the GameCube and 360 controllers are my favourites, both for different periods in my life.
When I was about 12 the GameCube controller had the perfect shape for my paws. Now, I am 19 and my hands have grown quite a bit, hell that's an understatement to say the least. And nothing fills those claws up better than the bulk of a 360 controller. I'm used to the PS3 controller now (due to my 360 dying) but it'll never fit in my hands as well as the 360 one. Simple ergonomics really.
Oh and don't forget about the horrible triggers on the DualShock, I'll never get used to those.