Probably the xbox 360 controller followed closely by the Gamecube Wavebird. Wireless was pretty cool back then. I also agree with the posters above, the Dpad on the SNES has never been matched since. Mjght have to do with TVs not being CRT anymore and most people playing emulators which can be laggy as shit. Old systems on newer TVs usually sucks too.
I'm a bit of favoritism to the PlayStation controller as that is my 1 and only be all top gaming controller. Though my first held controller WAS a NES but I'm also fair to say SNES also and the Wii controller extension that looks like a nes/psn controller combined. The Wiii wheel was pretty cool in you just take a Wii controller insert in middle and done.
I still need to track down a vintage SNES pad. Sadly, all I have is a replica. At least it's nice quality.
SNES, Gamecube, Dualshock 4(1-3 are good, but 4 was a noticeable improvement), 360/One, Switch Pro Controller, and the Hori Pro Joy-cons(I can't go back to regular joy-cons now)