There are some controllers I haven't used, but from the ones I have I'll share what my favorite controller is.
The first controller I used was the N64 controller. Back then I had no issue with it, I liked it but it wasn't durable. The control stick would wear down so easily. Aside from that, an ok controller, and an interesting design, it was ok to hold but only as long as you held it with your hand on the middle handle, it just felt weird trying to hold it with just the left and right handles.
The SNES controller was pretty simple, it was decent, easy to use, I've actually never used a NES controller, but I'm sure the SNES controller was appreciated over it.
The Duelshock 2 was so flimsy. Usually people complain about how things in a controller are too far apart, well with this controller they felt to be crammed too close. Those big clunky control sticks stuck so close together, lol! Oh such memories! I mean yeah they were big and easy to get your thumbs on, but they had no grip and felt slippery. And I was a kid who would get sweaty hands after holding a controller for awhile so it was a love/hate relationship. I loved my games on the PS2, I just hated the Duelshock 2 Controller.
I didn't have an Xbox, but a friend of mine did so I did get ahold of The Duke. Prime example of everything positioned weird, and it was just too big. It was a big reason why I had no interest in buying an Xbox.
The Gamecube Controller was amazing, and its design is still great to this day. It was the first controller I fell in love with because it is so comfortable. Everything is spaced just right, that big A button, those huge L and R buttons that your fingers just sit on perfectly, and the controller was comfortable to hold.
The Xbox 360 Controller was amazing as well. I honestly can't find anything to complain about with it. The buttons were spaced perfect, it felt comfortable, I loved it just as much as the Gamecube Controller.
The Wiimote and Nunchuk pairing wasn't exactly bad. I actually thought the D-Pad was ok located above the A button, and usually if you needed to ever press it while using the nunchuk it was just to press Down. But shifting my thumb up to the D Pad was easy enough, I feel. The 1 and 2 buttons were out of reach. I don't ever recall needing to press them when the controller was paired with the nunchuk though. And I have to admit, the wiimote was comfortable to hold, so was the nunchuk. I think it was pretty good, although I hated trying to play games without the nunchuk connected. Playing with the wiimote that way was really the only time I think the 1 and 2 buttons really served any purpose, because they replaced the A button, and the B Trigger.
I hated the Wii Classic Controller. I much prefered the Classic Controller Pro because it actually had handles and was comfortable to hold. That, and the Z buttons were shifted to be underneath the L and R buttons. The control sticks were also spaced apart better. I would hook up my Gamecube controller instead while playing VC games, even the Wii Pro Controller wasn't great.
I guess we have to consider the Wii U Gampepad a controller, and in that case don't we have to add in the DS and 3DS? Short story, they all 3 are decent. Wii U gamepad is just too big though. The DS was alright. My biggest dislike of the 3DS was it's control stick. I mean it works fine, it feels fine, but for me idk why, it doesn't feel like it could handle some rough heat of the moment gameplay.
The Wii U Pro Controller was great as well, before the Switch Pro Controller I would have said it was definitely in my highest tier of fave controllers. I'd say it is maybe slightly better than the 360 controller, in fact it's design is practically identical. Like
@Cfrock pointed out, the controller has an amazing battery life too.
The Switch Joy Cons are ok, but I don't like using just one, even though it's so small and you can actually connect it to your phone, or even a tablet, to play mobile games. Problem is you'd have to be playing a game that doesn't require many buttons. I can tolerate using the Joy Cons connected to the cradle, but I'd rather be using them unconnected, if I even use them at all.
The Switch Pro Controller is much better to use and I'd say it's even a step up from the Wii U Pro Controller, I love the offset control sticks, it makes it feel even more like a 360 controller. Plus like the Wii U Pro Controller it has a long battery life. It's design also looks more unique than the Wii U Pro Controller, it doesn't look like a copy of the 360 controller although it still kind of is. A step up for sure.
The Duelshock 4 is also on my higher tier of controllers, and I'd chalk it up amoung the Gamecube, and Switch Pro Controller. For a company that has historically had bad controllers, it's so suprising that they would end up making the Duelshock 4 into one of the best controllers available currently, arguably the best controller to date.
So yeah, toss up between the Gamecube, Duelshock 4, and Switch Pro Controllers for me. In the end I'd say the Gamecube Controller remains the pinnacle. I'd love to get an official wireless compatible Gamecube controller. It's sad that all we have right now are still only imitations not even made by Nintendo.