1. Nintendo Gamecube: With an exception for fighting games, it's my most preferred controller. It fits well in my hands, the buttons are well placed(for the most part), and is an all-around, well designed controller.
2. Playstation 2: With what is practically a Super Nintendo controller with handles and an extra set of triggers, what's not to like about the Dualshock 2? The D-Pad, that's what. But a bad D-pad doesn't hinder the quality the controller has offered since the PS One
3. Sega Genesis: Because if I put the Super Nintendo controller on this list, I'd be repeating myself. Just kidding, the Six-Button controller, while not needed for most games, was a great improvement of its Three-Button brother. I can't imagine playing 16-bit fighting games any other way(actually, yeah I can, but that's besides the point).
Honorable Mention: Nintendo Wii. A controller that feels comfortable while holding it forward and sideways? Good show, Nintendo. Now only if it had an internal rechargeable battery.