It's hard to say, honestly the NES controller is the most famous I'd say, but the damn thing hurts your hand after a while. SNES I spent a lot of time with that little buddy and it still brings a tear to my eye holding it (or by design the Classic Controller) and playing some SNES games. The N64 controller was odd at first but when I started playing some games it worked really well and felt natural, on the flip side GC felt natural from day one but sometimes games didn't take advantage of it as much.
The Wii controller is probably the most natural and versatile... plus the advantage of a number of options to play a game... it's hard not to pick it, the others would be picked because of nostalgia but I gotta say the Wii remote can be as complex (able to attach classic controller) or simple (Wii remote on its side) as you need it to be and increase accuracy (FPS) or fun (Wii Sports) with games.
MaxwellGT2000 - "Does the amount of times you beat it count towards how hardcore you are?"
Wii Friend Code - 5882 9717 7391 0918 (PM me if you add me), PSN - MaxwellGT2000, XBL - BlkKniteCecil, MaxwellGT2000