Probably the Gamecube one.

Umm... that would be the PS1 controller before the dualshock. It had more room for my hands and, as such, is more comfortable than any dualshock to me. But I can't say that dualshock is the "classic" one.

Gamecube

2D games: Saturn pad
3D games: Wiimote+nunchuck

360 wireless. (old school fav is the NES controller)

Yeah you got me on a technicality so I'll give credit to you; but the Dualshock did make its appearance later on with the PS1 I believe. 

All time? SNES. It's hard to explain unless you were coming off the NES and dabbled with the Genesis, but the SNES controller just felt perfect in every way.

Current gen? Wiimote with Wii Motion Plus (soon to be standard since they stopped selling wiimotes by themselves).

Without WM+ I'd have to go with PS3 controller over 360 because of the better d-pad and the severe right-hand bias of the 360 controller.

Xbox 360 controller. Love the joysticks where they are, not too heavy or light, chatpad goes great where it plugs in, and triggers are great.

My favorite controllers

8-bit 1.NES(Famicom) Pad
2. SEGA Master System PAD

16bit 1.SNES(Supper Famicom) PAD
2. SEGA MEGA DRIVE( GENESIS) PAD but 6 Button PAD best for Fighters

32-bit/64-bit 1. SONY Dual Shock
2. SEGA Saturn but best for Fighters
3. N64

128-bit 1. SONY Dual Shock 2
2. Gamecube
3. XBOX Model S based on playing on friends XBOX
4. Sega Dreamcast

Current Gen 1.SONY Dual Shock 3
2. XBOX 360 based on playing on friends 360s

but when I get a Wii my number 2 will probably be thr Nintendo Classic Controller Pro my all time favorite is a tie between DS3/SNES as all purpose Controllers and
SEGA MEGA DRIVE(GENESIS)/SATURN for Fighters.