I'm just going to talk about currently released and supported console controllers. It's easier than trying to remember years of gaming controllers.
Best has to be the 360 controller. Both analog sticks are in the right spot, the triggers are perfect, and all four face buttons use very different colors so there's no confusion in QTEs (unlike the Dualshock, where some games draw the buttons so small that you can't see if it's a circle or a square, and all you can see is some kind of reddish/pinkish color that could be either button). Only problem is the d-pad, but it's rarely used so I can forgive it. Plus, it's apparently somewhat easy to take the controller apart and fix it if you wanted to.
Worst has to go to Sixaxis/Dualshock 3. I actually like the Dualshock overall, but for the 3rd version where they decided to make changes to it, they changed some things for the worse and didn't change other things that needed it. Leaving the left stick down at the bottom was stupid, and replacing L2 and R2 with those awful "trigger" things was madness. Hey Sony, triggers curve outwards so that your finger can rest in the curve, not inwards so your fingers slip off. Thankfully you can get some plastic snap-on triggers that make L2 and R2 proper triggers. Also, this just in: segmented d-pads STILL suck, especially when you end up making the buttons too far apart. Sure, the Dualshock d-pad works great... Until you need to hit a diagonal. Then the buttons are too far apart to hit two at the same time easily, and since they're all separate, you can't just stick your thumb on the middle of the pad and slide it over in the direction you want. Again, it's rarely used so it's not a big deal, but it sticks out to me that if they wanted to change things on the controller for this version, that was something they should have changed. Also of note, tossing in cheap motion control at the last minute after seeing the Wii Remote. The sad thing is that some developers still haven't learned to go Playstation Move or no motion controls at all, so you get shit like having to use the motion controls to turn some wheel in Killzone 3 when using the Dualshock. Motion controls to turn the wheel is fine if you're already using Move to play, but if you're using a Dualshock, leave it all to the buttons and sticks please!
So yeah, for taking a controller had room for improvement but instead not improving anything while making it WORSE, Dualshock 3 gets a big thumbs down from me. Again though, I still like the controller. It's the worst out of a set of controllers that are all quite good. It's like a 7/10 while the others are all 8's and 9's, and this is a real 0-10 scale where 7 is really good and not shitty like in mainstream game review scores.
Honorable mention goes to the Wiimote for having a speaker that is somehow worse than the speakers in the original GameBoy. And because of that shitty speaker, the d-pad is a bit too far towards the top of the remote, making reaching for it (especially the up button) in games where you hold it vertically a bit awkward. Take out that stupid speaker and bring all the buttons but the power button down a bit, and bam, it would be so much better.
Here's my homework for Microsoft and Sony: Go get some Wii Remotes, Classic Controllers, DSis, and 3DSs. Use the d-pads. Use them a LOT. See how wonderfully they work (except for the aforementioned Wiimote problem, but that's placement, not the pad itself). Study them carefully and try to make d-pads like them for your next controllers.