Worst ones:
-N64: This has been repeated so many times, but seriously, on what kind of controller would you made a third of it useless? That wasn't the case for every game, but it's still a ridiculous design.
-any controller with a number pad for buttons: I think the Atari 5200 comes to mind for this, so it's especially bad when it doesn't work.
Best ones:
-NES: Keep it simple, stupid.
-Gamecube: Having the A button be a huge one in the middle of three smaller buttons was a weird idea. Still, it helped to know what the main button was for your most important action.
EDIT:
Honorable Mention goes to the Wiimote for sheer versatility, although I'm not a huge fan of superfluous motion controls that could just as easily be mapped to buttons (like spinning in Mario Galaxy).