Top 3:

1) Gamepad
2) Gamecube
3) N64

N64 was, imo, their most innovative (Z trigger, analogue, multiple possibilities for holding)
Gamecube was, and is, the most comfortable controller
Gamepad is the pinnacle, IMO, of the Nintendo design ethos. Literally only thing it is missing is analogue triggers. Which is no huge deal.

Wii U, I think.

I am still a fan of motion controls, so WIIMOTE+NUNCHUCK.

WHERE IS THE WII BALANCE BOARD!

Seriously thought the GC controller was excellent. I mean seriously it might be the highest selling controller this Holiday season. That says a lot.

Also stop with the N64 hate :(

Easily GameCube, that controller should've become their standard. It really needs a modern facelift though, then it would be solid.

Best = Wii U Pro.

Best (for its time) = SNES Gamepad. It was far beyond anything before or during its time. It holds up great to this day. The U Pro is better, with more ergonomics and analogue sticks, but it's only slightly better than alternatives on XBox or Playstation. And it's not innovative at all, just solid execution. And it could use analogue triggers.

I find the concept of the Gamepad brillant, what hurt is the lack of shoulders analog triggers.

My choice would have to be the Wii Remote since I'm a soccer mom.

gamecube all the way. still one of the best controllers ever

I'm definitely with you on this.  The freedom that it gives is amazing...and you somehow feel more engaged...particularly on a game like Metroid Prime.