Xbox 360 controller. The GC controller is also nice.

I've played a lot of PS2 games, and the Dual Shock controller is just too small, and the joysticks are too close together. They're fine for kids like leo-j, but a grown man's hands fit the GC or 360 controllers much better, and having the left joystick higher than the right joystick allows for the thumbs to cross without bumping into each other.

no question 360 controller u dont even realize its in ur hand

 I, for one, have always found Playstation controllers to be very uncomfortable.

I like the SNES contoller, but also the n64 and gamecube

SNES pad for my money. There really isn't a flaw to point out. Excluding advances that were made in future generations (wireless, analog sticks, six billion buttons) it's fantastic.

I'd put the 360 controller a close second.

360 is in my opinion is the best controller with GC coming in with a close second.

@Leo-J

Many people don't like that the thumbsticks are next to each which I can agree with. I also don't like using L1 and L2 for shooting in some games.

 okay okay i admit i never touched one, i got xenophobia.

I just love the freedom of the Wii-mote. I did also love the smaller original XBOX controller.

The Sixaxis controller is nice, but Its a bit light. Dualshock 2 therefore is my preference. I understand people complain about the analogs being beside one another, but for certain games (sports games especially) I still prefer the use the D-pad which is positioned nicely on the dualshock.

Trying to use the d-pad on the xbox/gc controller is alot harder.

Yeah PS control sticks are awkward. I'm not too keen on the d-pad either, i like the layout [middle of pad hidden] but you seem to have to press hard for anything to happen.
My vote would go to GC.
2nd is N64
3rd is PS [dual shock]
4th Wii remote
5th SNES
6th Megadrive
7th X-box [only one that was bad enough to affect my enjoyment, those buttons are painful]

^that was in terms of comfort.
In greatness terms;
1st Wii remote/nunchuck
2nd N64
3rd wavebird*
4th GC
5th dualshock
6th SNES
7th Megadrive
8th x-box

Those lists are based only on ones i have had experience with btw. In comfort terms i think 360 may be high as people seem to praise it [could just be they have no feeling left after using the x-box one] and six-axis would be high in greatness [same as DualS in comfort]

*included with GC in comfort.