The GameCube controller is my favorite. It fits perfectly in my hands and the buttons are in the right places. The Wii U pro controller is a pretty close second.

Add me to the Wii U pro controller camp.
I hope the NX have a similar one.

I had a lot of issues with wired GC controllers. I actually was getting quite pissed and tired of sending them back to Nintendo. I would ensure everyone had washed hands and no one was playing rough with the controllers. The damn b buttons kept sticking on me. They would get jammed down and barely work as intended. The c stick (yellow stick) would also start messing up (notice right away when playing Melee because that controls the tilt of the character select screen). I sent them a final email saying what ever you do make sure your next controller doesn't suck as bad as this one.   That is how the Wiimote + nunchuck were born.

I eventually tried a Wavebird.  I never had a problem with b button sticking or c stick going out and still have 4 Wavebirds.

The GameCube controller. It's very comfortable and I love the analog triggers, probably the best out there.

N64 for me. Spent hundreds of hours on it and it felt so good. I was unstoppable in FPS games and is the reason why I'm a southpaw control guy today. OH and Goldeneye dual controller setup = nothing can compare.

GameCube