NES: Obviously this controller is a classic, and a huge improvement from the controllers before it (why did so many controllers have numeric keypads? i mean really?) but by no means the best.
Master System: Same as above, but gets less points for originality since they basically ripped off Nintendo's.
Turbo-Grafx 16: ^
Genesis: Way more comfortable than the SNES controller, but not as functional =/
SNES: Compared to controllers now, this thing feels awful, but it was awesome back in the day. Especially because of the shoulder buttons. Nintendo was always ahead in terms of controller innovation.
Sega Saturn: I've never used it but I don't think I want to. I think that might be the stupidest looking controller I've ever seen.
DualShock: This is pretty much the perfect controller. Good comfort, good button placement, good functionality. It doesn't excel in everything but it doesn't need to. It just works no matter what.
Nintendo 64: This controller had a lot of potential but nobody really used it the way I think it was intended which made for horrible controls in a lot of games, so that kinda ruined it =/
Dreamcast: Obviously an improvement from the Saturn, but awful compared to what was already out there. It felt awkward and weak, like it was made of cheap plastic. The VMU thing was kind of cool though, I guess.
Gamecube Great, but kind of weird. I didn't like how the A button was so prominent and the D-pad was virtually unusable because of its size.
Xbox: This thing is like holding a loaf of bread. It's comfortable but not very intuitive, I remember having to look down a lot to make sure my fingers were in the right place.
Xbox Controller S: An improvement, but easily outweighed by the 360 controller.
Wii: The controller that spawned a revolution, kinda. After Wii put this baby out, everyone jumped in on the motion control craze. It makes a lot of games weird to play (Super Mario Galaxy being a prime example of this) but it works so well for its other games, and its number of uses is through the roof so it's easily one of the best.
360 Controller: This would be my favorite controller by a long shot if it weren't for the D-pad. I don't get why Microsoft made it a POV switch; it doesn't feel like a real D-pad. It makes it kind of awkward to use with games where a D-pad is more sensible. Other than that, its button placement is perfect and its comfort is second to none.
In the end, I chose DualShock, Wii and 360. Between them I'd probably pick the DualShock controller as my favorite, simply because I can never remember ever having a single complaint about it.