The genesis controllers were pretty bad.

Too small, not ergonomic, cheap feeling triggers, sticks too loose and too close together. 

A tie between the Xbox One, the Xbox Duke, and the Wii U game pad. That being said the Xbox One's controller was the only one to cause extreme levels of discomfort. The Duke and Wii U game pad just takes some adjusting to get used to.

OP you're nuts, Gamecube controller is superb. I also really like the NIntendo 64 controller- I always felt like the reason so many people must have not liked it is (possibly?) they were holding it wrong and attempting to put both hands on the outside (left and right) of the controller, rather than putting one hand on the center and only one on the outside. For 9/10 games that's how you hold it. Although its analog stick was pretty disatrous in terms of getting loose after a while

controllers I like include: SNES, NES, any Playstation Dualshock. OG Xbox is a pretty damn comfortable controller. 6 button Genesis is nice.  Gamecube is the GOAT controller in my eyes. best analog stick of all time, high quality materials, perfect sized nub for the c stick, extremely satisfying feeling L and R triggers (unmatched by any other controller I think) etc.

controllers I'm in the middle with: Dreamcast (not uncomfortable, but not necessarily inutitive and a weak analog stick), standard Genesis controller (mediocre, not great), OG PS1 controller (no analog stick), Turbografx 16 (looks awful but is middling, works well enough for most things)

controllers I dislike adamantly: Master System (buttons not mega responsive, somehow fairly less comfortable than the NES controller despite being very similar in shape, maybe cheaper plastic?).  Wii Controller (awkward asf for anything not a party game, Twilight Princess with the Wii Mote is a nightmare compared to playing it on the Gcube). Atari 2600 joysticks = hate. Sega Saturn has a pretty bad controller (plastic feels cheap, buttons do not pop back and respond that great, break easily, etc.).

if we're talking third party controllers- a massive # of Madcats awful variants for the PS1, Gamecube, N64, etc are quite terrible and uncomfortable and have awful analog sticks. Hori has some pretty great stuff for Nintendo for most generations but they are a bit of a rip off.

that controller is immensely more awkward than the Nintendo 64 standard controller. I can't emphasize enough if you simply hold the Nintendo 64 controller correctly, for right handers - (right hand on the outter right side, left hand in the middle section), - that most games on the Nintendo 64 control extremely intuitively 

100% agree on this one, for the same reason. Second up would be the first few DualShocks, before the DS4. Too small for my hands, and the convex analog sticks are uncomfortable for me.

Aside from 3rd party jank junk, the worst I've used is either the Power Glove, U-Force, both the OG Xbox controller & Dreamcast controllers.

All Dualshocks Controllers
Wii Classic Controller
Original Xbox Controller

Basically any controller with the dual analogs both on the bottom.

Man, it must suck having unsymmetrical hands.

@ OP

I'd have to say the original Xbox controller (the Duke) for just being WAY too big to use comfortably.  And definitely the N64 controller.  Any controller you can't reach 1/3 of the buttons without grabbing a 3rd grip, which then disallows you from using the analog stick and trigger button, is shit.

how are my hands unsymmetrical?

When playing a game, the buttons one uses the most are the left joystick and the right buttons. Thus it is most comfortable to have your hands resting evenly in the same place. You know, symetrical.

But playing on controllers with the joysticks both down below, my hands start to hurt after an hour or more. Kind of like when playing on a small controller like a 3DS or something. My hands are cramped and in an awkward angle. 

If your hands are rensting comfortable on the conrollers, you thumbs are resting nicely more vertically. YOu have to move your thumbs down to the joysticks on those controller I listed. Thus just having your thumbs in position, let alone using them, is working your muscles. It's a less natural position.