I'm not going to place any of the few that I list in order.

-Mouse and Keyboard
-Dualshock (PS1, PS2, and PS3)
-Xbox 360

I don't mind either Dualshock 3 or Xbox 360 designs.

The hands down best and most influential is...

The SNES pad. It perfected the NES pad and became the template that most gaming systems used going forward.

At number two, the N64 controller. Adding an analogue stick and eventually 'rumble' made the controller more responsive and provided feedback back to the user. Both features were eventually copied by the world plus one.

At number three, the Wiimote. Why not number one or two? It hasn't lived up to its promise yet.

Moving right along, the Dreamcast controller. Pretty much taking something from everyone and putting it into one large rigid mess. The cord extended from the bottom, two add on slots, and it was anything but ergonomic. But sadly no one has ever copied the VMU or last least added a screen/display to their controller.

And in number five, the Wavebird. The first first-party wireless controller. The only thing lacking was rumble. But the batteries lasted forever and it felt just right.

1. dualshock 3
2. dualshock 2
3. dualshock
4. playstation non-analog controller
5. N64 controller

1) Gamecube controller
2) SNES controller
3) 360 controller
4) N64 controller

These ratings are based on comfort and ease-of-use. I find the Gamecube controller the most comfortable, though the D-pad is too small.

I dislike the analog placement on the DC pad, and it didn't have enough buttons. I've never liked any iteration of Dualshock.