For me it's either the Dual Shock (Currently DS4 cause it's bluetooth, I use it on my PC), or the NES dogbone controller. I really liked the Dogbone, to me it was a perfect melding of a next gen controller and NES. The dpad didn't hurt anymore and it had a ergonamic design.
The dogbone is pretty terrible in my opinion, same with GameCube and PS1/2/3. The DS4 is alright, but nothing compares to the Xbox One controller; it's perfect. The second and third best are Xbox 360 and SNES for me.
This is a hard question for me. So many great controllers. I'm sure we can all agree that the controllers from Generation 1 and 2 systems are garbage haha! Just kidding, I do like the Magnavox Odyssey 2 controller. I absolutely love the Xbox One controller and the DualShock 4. I use my Xbone controller on my PC and love it. I use the DS4 on my PS4, PSTV, and sometimes my PS3 and it's amazing. Super comfortable on both of those. I also like the Wii U Gamepad and the Vita itself. The Saturn model 2 controller is nice too but I haven't used it much. I also like the Xbox 360 and DS1/2/3 controllers. Although the DS3 seems more flimsy than the previous DS controllers. Nowhere near as bad as the Sixaxis though. That will break if you squeeze it to hard! Oh, I can't forget the Atari 7800 joystick! *picks up 7800 joystick to play Pole Position II* Nevermind, just remembered how bad it is... *shivers*
I would like to suggest a combination of the SNES controller CABLE spliced with a Sega Saturn Model 2 controller. Such a silky smooth cable with such a sassy beast of a controller. And I'll take my controller in skeleton grey thanks! That said, I own an 8bitdo SNES controller... it has no cable :\
I like the Japanese 6-button Mega Drive-controller the best, but the Saturn-controller is a very close second. Nothing comes close to matching these, unfortunately.
The Gamecube, hands down. I like how even though it's a huge leap from the N64, it's also backwards compatible with all the buttons still there, although somewhat transformed, like the C buttons now being a stick for example. It's very comfortable.
I would say the Gamecube's Wavebird, hands down the best wireless controller I've ever had. Perfect weight, great range, and very long lasting battery life. Other than that, I find the Xbox One controller to be very good as well.
I think we're going to find a lot of people saying this one. You know what we WON'T see? N64 controller. Also the DC controller and the Duke. Honestly, the Xbox ONE controller is quite solid. Besides the DS4, I'd go with that one.
Hey, the N64 controller isn't that bad lol! Works great for me in Mariokart 64 and Pokemon Stadium 2. Also, I don't think the DC controller is as bad as everyone says it is. It fits my hands ok. I do feel like it's missing a second analog stick though. Would make playing Half-Life easier. Maybe I think that because I haven't used it enough.... *looks at dusty DC*
@MBMM fyi the N64 controller is my favorite. u_u' I have a problem with the japanese Saturn controller. I don't know why but I break this dpad. Must be how my finger grips on the pad. It just breaks too fast (months obviously) and I've never worn a N64 stick. My controllers are very well taken care of, so taking care is not the issue. The Joystick 3D (never broke one) is more durable at least for me. And it's comfortable too. (only issue of the 3d is a funny one: the digital pad of the joystick 3D is made of a weird plastic that "grabs" dust by itself lol, like a rubber-plastic thing, so store it in a closed place like a drawer, etc) The Xbox 360 and Xbox controller are very good too. Obviously the last Xbox 360 controller with the transforming pad is the best. It's hard to come back to the first pad after playing with the cross pad. But the most confortable is the Gamecube. It's ugly, but you can feel your hands happy when you hold it. I mostly like all of them, though.
Favorite "3D" controller: Gamecube, hands down; preferably wired. The Wavebird is a great wireless controller but 1) I like the heft of the motors in the wired controllers, and 2) I'm a competitive Melee player and I'm very paranoid and eliminate lag anywhere I can. (this is mostly a problem with Wiis moreso than Gamecubes from what I've seen but alas, many Melee setups at tourneys I go to are, in fact, Wiis.) Favorite "2D" controller: Saturn Analog controller. Yeah, it's designed for 3D games, but even without the analog nub it makes for a surprisingly comfortable and well-functioning controller for 2D games, despite (or perhaps due to) it being shaped like a five-year-old's drawing of the USS Enterprise by memory.
Never really had an answer now until I started to use an original Xbox Duke controller when playing the console again. There are other controllers, but none of them really fit my massive mitts like the Duke does and it feels glorious. It may not have the best D-Pad or button placement but I reiterate, it's the controller I grew into when growing out of others.
I got a saturn sometime ago and a 3d analog pad. Boy, that wasn't how I remembered it. I remembered the analog being smooth in games. But the analog part was plastic and pretty cheap feeling. I hope Sega was smart and made that rubber on the dreamcast. Still tho, no 2nd stick was also a mistake.