7th gen: 360 controller
6th gen: Dualshock 2
5th gen: Dualshock
4th gen: SNES controller

EDIT:

All time: 360 controller

gamecube controller

360 controller is the best controller ever.

Either Wiimote or N64 one.

NES and dual shock controllers for me, they both are and were "ahead of their times". I question the "logic" of people who like the wiimote because why in the world would Monster hunter 3 not support it if it was so great? Instead they created a "clone" of the dual shock and bundled it with the game in Japan. For some games the wiimote is a God send, but for the other games nothing beats a industry standard game pad/controller.

It seems like they are always copying Nintendo with the controllers.

NES makes the d pad and sideways controller, every other controller that followed did the same.

SNES made shoulder buttons

N64 revolutionized the analog stick (which Sony promptly released their own version for the Playstation soon after seeing how effective it was). And introduced rumble, a standard all controllers have built in today.

Wii remote introduced motion control, and Sony and MS are already demoing their motion controls.

It's clear who is leading the industry in terms of player input. I have to give Sony credit, however, for being the first to have 2 analog sticks.

And the first on consoles to use the camera for game play input.  Motion control definately was nintendo's greatest achievement to gaming.  Outside of that they all emulated what pc gaming had already established for anything else.

This article tries to make it seem like the Playstation controller (dual shock) came before the N64 controller. No mention of the PSX's Super Nes clone. The N64 controller offered a microphone, analog, and rumble. The "C" buttons were the precursor to dual analog. It was awkward, I admit, but the N64 was the "missing link" between then and now.

Yup, that's the truth.

Many people forgot what the orignal PS controller looked like before Nintendo brought out the N64.

one single analog thumb stick and a add-on for rumble for the N64 (what microphone was used for the N64?); Sony's "revision" of the first sony controller now dubbed "dual shock" had two thumb sticks and built in rumble technology.  Obviously looking at both layouts you can tell that sony's layout was far superior to that of the N64 during that generation.  But nintendo did have the rumble before everybodyon consoles (PC had all kinds of tactile feedback options, but of course we are talking about consoles).