My favorite controller has got to be, hands down, the Xbox 360 controller. I loved it from the moment I first laid my hands on my friend's launch 360 all those years ago. Its the perfect size, everything feels right where it belongs, nothing is hard to reach, the triggers feel like triggers, it just feels right.
The only downside it has is that sucky D-Pad.
As for a least favorite... well, I never really thought about it before so I'm not sure I even have one.
I don't like the Dualshock 3's triggers. No matter how long I play with it, I can't get used to them. I miss the triggers from the Dualshock 2.
Actually, I think I hate the Gamecube controller the most.
Not only did it have to follow the N64 controller (which I still love), but it only had one analog stick, the C-stick was annoying to use, I could never remember the difference between the X and Y buttons, and I kept forgetting where the fuck the Z button was.