Has to be any Dualshock... 3's the best because of motion functions.

Gamecube or 360. Both fit in my hands great with all buttons in comfortable reach. Both have some flaws (D-pad on both) but are overall well designed controllers.

The 360 controller should be immediately disqualified out of every one of these discussions.

Sorry, but if anyone thinks the D-pad on that thing is even REMOTELY feasible to play with, they are out of their mind. That or they haven't really played anything else.

My personal favourite was the N64 controller... the D-Pad there was too stiff though, and the stick could be unreliable after a few years. The stick itself was the best stick I've ever played on though, so that's why I give it a lot of points. The overall layout of buttons made it an almost universal controller for all genres. Again, the stiff D-Pad is what held it back mostly.

As for the best controller of all time, it's a rough choice between the SNES controller and the PS2 controller.

The SNES controller is perfect in every regard, but lacks analog sticks (since they just didn't exist back then). The PS2 controller is just a rip off of the SNES controller, but with two sticks and two extra shoulder buttons. The sticks on the PS2 are too stiff/sensitive which makes it hard to aim accurately (without the use of auto-aim).

Furthermore, the PS2 has two different kinds of D-pads depending on the revision. One has softer, glossy D-pads that allow for easier "thumb sliding", while the other has a harder, "grip" based D-pad that will hurt your thumb after continuous hard play (all PS3 controllers feature this kind of D-Pad).

It's quite a hard decision if the question is for "of all time". SNES is perfect, but lacks sticks, PS2 is near-perfect with minor flaws. Now if the question was "best controller for its time of all time" or something-er-rather, it would be the SNES, as it had no flaws compared to all subsequent controllers that all have at least one flaw.

dualshock hands down. i'm in my 30's and i've had or played them all. dualshock is easy on the hands when your doing a hado-ken.

360 all the buttons you'll ever need in good locations.

EDIT:

#1 Wiimote/nunchuck

#2 Wavebird (Nintendo's Wireless GC Controller)
#3 SNES
#4 Logitech Wireless Dualshock 2 Controller

I'll second that the 360's D-Pad DQ's it from consideration. If the D-Pad was ok, this would be an outstanding controller. But it's not.

The SNES controller was bar none the best controller.

2D- Saturn
3D- Gamecube

Xbox 360 is good too