A toss up between the Saturn (Model 2 controller), and the Gamecube controller.
Both work perfectly for pretty much any game you throw at them, unlike other controllers such as the N64 that only really make sense if you are playing Goldeneye, or Perfect Dark. They are also extremely comfortable, and not overly large (Original Xbox and Jaguar controllers are guilty of this). They also don't give you finger cramps during long play, which the Dreamcast does to me after playing Jet Set Radio for a few hours.
Both are the perfect controllers in my eyes.
Here's a handy chart (which is missing Wii U controller):
I hate to be a Nerd, but it's Missing a hell more than that...
Most notably, The Saturn, 3DO, Jaguar, Turbografx-16, Virtual Boy, CD-I, Fairchild Channel F, Neo-Geo, Neo-Geo CD, Amiga CD-32, Intellivision, and the Atari 7800 Controller.
That's not even including the very Obscure systems, and the Japanese only systems like the PC-FX.