Ever since I first got my hands on a Dual Shock (bought with Gran Turismo on the PS1), I have never held another controller that comes close. Two generations of PlayStation later, and the basic controller layout has not changed in the slightest.
Sure, the L2/R2 buttons are big and soft now, theres the "PS" button in the middle, and maybe SixAxis is a bit rubbish, but in terms of pure comfort and good ergonomic design the DualShock series of controllers, well they just fit.
They are the gaming equivalent of a pair of silk RAF pilots' gloves compared to the Xbox's tough, but big and chunky skiing gloves, or the Wii's clumsy, shit-for-anything-requiring-precision boxing gloves.
I also find that I can play the same game on a PS3 and an Xbox360, and will always do better at the PS3 version - I put this firmly down to my comfort with the controller.