I find the Classic Pro slightly more comfortable to hold than the GC one, and the buttons have a better feel to them (though I didn't have a GC last gen and I've only played a bit with the GC controller on the Wii, so not really used to it).

And while I find the Wiimote + nunchuck the most comfortable to hold option, I find the + pad slightly awkward to use and the +/- and 1/2 buttons even more so. If those are not used a lot in the game, and not used at important moments, it's fine but otherwise I go for other control options, if there are any.

Gamecube one. It fits so perfectly in my hand

This is a though one.
I loved the N64 controller and I love the Wiimote + nunchuck too.
The rest of them are not bad at all either, specially the classic controller.

The Remote & Nunchuk combo, by far. It's just too darn comfortable.

As for traditional controllers, the 'Cube one beats the hell out of everything else out there, ever, including current gen controllers.

wiimote + nunchuk for me as well.

not even because of the pointer (which is also great in a lot of situations) or because its revolutionary, but because it really like the split-up design.

i was always a pc-guy. with wasd+mouse i can hold my arms in a comfortable position.... i find the classic gamepad very uncomfortable because i have to always have my hands so close together.
the wiimote/nunchuk is the first solution where i can place my hands separately, and it feels great.
i never had a NGC but wanted to play wind waker after i finished twilight princess and thats when i bought a NGC pad... the game is great, but i still can't stand pads... although i like the button positions on the NGC pad and that the buttons have different shapes. makes it easier to "learn" the layout when you are not used to hit yet.

plus: the wiimote+nunchuk doesn't have 2 analogue sticks... a layout i hate with a passion. after playing zelda on wii, aiming with the bow on NGC was so horrible that it almost made me stop playing. yes, i'm spoiled ;)

Gamecube controller, it was perfect when playing resident evil

SNES. The controller so good that almost every controller since has been a copy of it.

Gamecube controller, it's the best designed, most comfortable controller in history. Wavebird is all that and BEAUTIFUL. Really, it's the best controller. The Wiimote is good too. Actually, I think Nintendo owned every other company controllerwise in each gen...

1.Wii
2.N64
3.wavebird
4.Snes
5.Nes

Wii > SNES > N64 > GC > NES

NES gets last because although it is an awesome controller, the SNES controller was just so much better. I thought the GC controller was meh, as it had a crappy d-pad and really odd button placement for a/b/x/y