I never liked the N64 controller. Who ever designed that thing probably never tried using it themselves, or was a mutant with 3 hands. The control stick and Z-trigger are poorly placed, so you had to play it with one hand in the middle of the controller, one on the right side, and that just feels so damn awkward.
The funny thing is that Nintendo's next controller, the Gamecube controller, is probably one of the best I've ever used. Just something about it is so right. Sadly, one of my 3 Gamecube controllers is semi-dead; I've used it so much that the C-stick is always freaking out, and the control stick occasionally has a mind of its own. Poor thing...
Most of the other controllers I've used are pretty good too.