in terms of comfort (and of the of the ones i have used of course)
GameCube - N64 - PS (any they are all the same) - Wii - MegaDrive - SNES - X-box (not sure whether it was big or small)
my fave has to be the Wii remote though, even if it's less comfortable (though the nunchuck is perfectly comfortable)the shortcomings of some of those controllers are these;
GC- the space for the index fingers for the shoulder triggers wasn't quite long enough to hold my fingers flat (though i do have quite long fingers) and the d-pad was a bit small for me, and i have quite thin fingers as well.
N64- life of the control stick and i suppose the irrelavance of the left hand side, but that's not much of a problem
PS- don't like the round reticule the control stick is in at all.my thumbs seem to have to stretch too far to get to the control sticks and i always seem to have to press really hard on the d-pad for anything to happen... oh and it seems by far the worst for making my hands sweaty (the GC is the best for this)
X-box was a bit too big (now i come o think of it i reckon it was the smaller one as well) is has the round control stick thing and the main coloured buttons are incredibly uncomfortable to press, had i properly owned an x-box i think i would have developed blisters.