The Keyboard and Mouse wins by a long shot as the best controller ever.

gamecube controller :), the best :), I never tried the wii one, so I can't say nothing about that

Wiimote + Nunchuck

2nd: Xbox 360 controller. Which is pretty decent since it comes off the back of the worst controller ever made, the original Xbox controller.

When I pick up a Playstation controller, my thumbs naturally go to the D-pad and the four primary buttons. However, to use the analog sticks I have to move my thumbs out of this natural position. It changes my entire grip on the controller and makes it much less comfortable to use.

Also like the wiimote and nunckuk

Keyboard + Mouse (and Microsoft Sidewinder for flight sims)

 Yeah the D-pad is harder to use on the Xbox and GC controller, but what's more important?  I'd say having the analog stick where the D-pad is on the current Playstation controller would definitely improve.  It's likely you only like using the D-pad for sports games and such because it's in the comfortable position...where the analog stick should be.

You caught me, Leo.  I've played through 40 hours of FF8, unlocked all the ships in R-Type Final, and finished Gradius V without continuing, all without ever touching a playstation controller.

N64... until this gen, now I don't know if I prefer N64, X360 or wiimote...

 Well to be honest, I dont have mammoth hands so the analog positioning on the dualshock controllers is quite alright for me, so a good analog and great d-pad > great analog and shite d-pad positions personally.