hmmmmmmmmmm. . . .
I'm fine with the Dualshock 2 and Sixaxis. I really like how the Sixaxis doesn't weigh that much, but it could use some rumble (however, too much rumble like the DS2 has in some games is bad and overpowering). Heh, I did have an issue moving to the original PS1 controller to the Dualshock 2, but that passed and now it feels weird going from DS2 to the PS1 controller.
I'm also fine with the Xbox (360) controller. I kind of liked the original (HUGE) Xbox controller and I hated the remodel, especially their curved buttons which killed your fingers in pressure sensitive environments. The only thing that really kills it is the D-pad, it's terrible when you need it and I hate using an analog stick in place of the d-pad for navigating menus and such.
I dislike the Gamecube pad because of it's small D-pad and c-stick nub and especially the Z button. I also dislike how thin it is to wrap your hands around, it feels like my fingers are stuck in position once I let go of the controller. Other than that, it's okay.
I'm not sure about the Wii-mote either. Waggle is more or less annoying at times and kills my wrists and elbows after only a little while of play. I also don't find the button layout very interesting and sort of uncomfortable (especially if you have to hold the Wii-mote in both hands).
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Keyboard and mouse it is!
Actually, I liked the Guitar Hero controller (somebody else mentioned this)