I really like the Xbox 360 controller for gameplay. My favourite retro controller was probably the Megadrive one.

It took me a while to get used to it, but now I think the 360 pad is probably my favourite.  It's comfortable, all buttons are accessible and have a nice positive feel and, since the move away from the standard cream colour, they look pretty nice too.

All time favourites would be the SNES pad, and Cruiser and Quikshot 2 joysticks.

I liked the Quickshot 2, although on the Spectrum I actually used the Cheetah 125+ as it had the extra plug for 128k machines. I never liked the SNES pad though.

The Xbox 360 pad is certainly a million times better than the horrible PS3 controller

I loved the original 'Zipstick'.  It was great on the C64 and Amiga.  Maybe on other machines as well.  The firebuttons were so positive and 'clicky'.  A really good feel to it.  Good stick movement as well.

As for for an analogue stick, well - the 'Gravis Joystick' for the PC was great.  Really good feel to it and well made.  Just a shame that it didn't have a 'hat function', that would have made Tie Fighter easier. 

Top 2 are easy but 3rd is more of a live for the system than the actual controller itself if I'm honest.

(1) Megadrive

(2) PS1

(3) Controller I used on my Atari 800XL.

I'd actually have to say now as I can't have the 360 or xbox slim controllers that my favourite is probably this:

the first Saturn controller was underwhelming and flimsy to me so to get two of these recently and for them to be of such good build quality and comfortable design I'm really ashamed I didn't buy them sooner. I had the good awful other saturn controller with the shitty shoulder button that went wrong within 5 mins of touching it lol

That is nice! Has anyone played much with the big Saturn Controller that looked like an early DreamCast controller?

For me, it's a three way tie between the SNES pad, a 6 button Genesis pad, and the PS1 Dualshock. Honestly, though, I never thought the N64 controller was that bad. My only real issues with it are that you basically MUST have an adaptor for one, because of the button layout. That, and I wish the analog stick was smoother.