The eternally undervalued Gamecube Controller imho is by far the best in terms of comfort and dependability. Second i'd go xbox360 wireless, that fat battery pack in the middle and the stick button annnd the control pad all make it inferior to the gamecube controller tho.
I don't get why people like the playstation controller to me its always been very uncomfortable and unimaginative. nintendo develops shoulder buttons sony puts 2 of them on their controller, nintendo develops controller joysticks sony puts 2 of them, nintendo develops l/r buttons sony puts 2 of them, so on and so forth