I'll throw some love in for the N64 controller. It was great at the time, too bad the analoge stick would get worn out so damn fast (between Smash Bros. and Goldeneye... sheesh). That was the first console i got more than two controllers for because i wanted/needed new sticks to be able to play the games. My only other complaint though is that my hands were too big and it sometimes felt uncomfortable with my left hand in the middle prong. It was rare that i'd feel cramped in there though, but other than that it played like a dream.
I like the SNES padthe best though if it comes to long hours of old school game time. it had the best dpad (i was mad N64's dpad was different) and the buttons were so easy to find by touch because of its simple layout. There were a few times my thumbs would get lost among the n64 controller but its never happened on with my SNES. The shoulder buttons were great too. It may not be the most comfortable thing to hold now though, and thats why i thought the classic controller would end up being my favorite controller ever...
i thought it would add the GC's comfy analog sticks to the timeless SNES design and have a more ergonamic form... but it doesnt. It feels like its always slipping out of my hand, which is crazy because its so damn small i feel like i'm playing my GBASP when my fingers touch. The shoulder buttons are kinda.. bleh to me. They couldnt decide to have GC style ones or SNES style ones so we got a weird hybrid that feels unresponsive in the older games.
The GC pad is also a good one, very comfortable but it has its flaws. I never liked the z-button positioning. I'll defend the face buttons though, i really really like them it was impossible to hit the wrong button with the way the buttons were all shaped.
I never understood the love for quadruple shoulder buttons.. ever since the PS1 they've felt so uncomfortable. I felt like i either had to learn to play with my middle fingers and leave support to only my ring fingers and pinkys, or fumble around with my index fingers up there and end up hitting the wrong button. The X-box controller had those triggers behind your index finger, and it was much more comfortable but again.. i could never get used to using fingers for those AND shoulder buttons at the same time.
I want a hybrid controller, one that combines my favorite features of the SNES, N64 and GC pads. I want the feel of the GC controller with the curved triggers and have the n64s Z button right behind the analog stick (like the N64, duh) and have the SNES face buttons. I might settle for all of the N64 face buttons but i miss X & Y

The D-pad could stay where it is on the GC style control (just make it bigger and more comfortable) and i guess the 2nd analog stick could stay.. i was never into dual analog so i could care less where that goes