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Im going to also say the Gamecube controller was the most comfortable controller vie ever used. Everthing just feels right, from the button placement to the shape. I especially loved the way the triggers felt.
Second place for me would have to be the Dreamcast controller.
GameCube, hands down. It's the comfiest controller I've used, especially the Chameleon controller you get at GameStop. It's a bit bigger than the regular controller, but for me, the ergonomics are so much better.
i wanna join the bandwagon and say GameCube was the best
in second is Xbox 360
and in 3rd is a tie between the WiiMote (holding it on it's side NES style) and the SNES controller
well, out of the ones I've used before anyway.