The best controller I arguably thing is the 360 controller. It just feels right to use in fighting games and fps. I like xboxs layout with the analog sticks.
Dualshock comes a close 2nd but was never a fan of the analog layout.
I find the n64 most jarring and I get that it was meant to be used differently for different games, but I still preferred the 3rd party options that took it closer to a standard gamepad.