My favorite used to be DualShock until the 360 controller came out. It's one of the few controllers that I have a hard time finding a single flaw with it. Triggers, analogs, buttons, comfort level, all pretty much perfect in my eyes.
The Wii controller is actually pretty lousy IMO. The "waggle" is cool but the actual design is pretty rubbish. Since there are so few buttons, many games end up relying on the D-pad and the +/- buttons for general play. The big problem is that you have to somehow hold the controller still (and pointed at the TV) while shifting your hand to switch back and forth to reach both sets of these buttons. Total crap and a weak design. The nunchuck is nice, though. No problems there.
Worst controller ever is the DC controller. I couldn't play it for more than an hour before my hands started cramping like crazy. The wrist angles on that controller were CRAP. Honorable mention to the dinner-plate Saturn controller. That was pretty craptastic, too. Why couldn't Sega get a controller right after the Genesis?
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