I think that the Gamecube controller was the best. It felt a bit more refined than than the N64 controller, and improved on the PS2 controller by putting the analog stick where the D-pad used to be. I liked the way it felt in my hands.
The runner ups would be the PS2 controller, and the SNES controller. The SNES has my second favorite controller. Incidentally, for those who praise the PS2 controller... let's compare, shall we?
Sony basically copied the SNES controller design, and added two analog sticks, two extra shoulder buttons, along with handles. Hardly innovative.
So while I like the Playstation controller... the reason I like it is because it feels a lot like the SNES controller, and is thus familiar.
I mean, just look at it. D-Pad on the left. Four main buttons buttons arranged in the shape of a plus sign on the right. R and L shoulder buttons (though the PS2 controller has two stacked on top of each other). The select and start buttons in the middle of the controller, from left to right.
Now tell me Sony didn't copy and slightly modify the SNES controller.