1)Wii-Mote/Nunchuk: Accurate and intuitive motion control combined with comfort makes this an instant number 1.

2)Gamecube: Everything seems perfectly proportionate (Minus the D-Pad) and has a very comforting feel in your hands.

3)XBox 360: Although I like the Proportioned Buttons of the gamecube, I also like the equally sized buttons of the 360... And the triggers are perfect! Other companies should definitely consider using something like them... However... the D-Pad is frustrating at times... and doesn't really fit as well as the Gamecube's controller.

4)SNES: Gotta love the original! Yeah, I know the NES was before this one, but as far as I'm concerned, the SNES set the path for almost every other game controller out there... The L & R buttons curve perfectly over the top, and the controller its self feels good, except I seem to hurt my hands when playing MegaManX (Tapping) and the Select and start suck really bad...

5)N64: For the First mainstream analog controller, they certainly did a good job... and the Z Trigger was awesome for Goldeneye, but it's awkward shape only seemed to work well in some instances, and the D-pad was almost completely made obsolete.I didn't like the L & R buttons this time around, and the c-buttons were too small... Then again... RUMBLE!

The next five would be something like this...
6) DualShock 3
7) Genesis Controller
8) NES Controller
9) Dual Shock 2
10) Dual Shock 1

1: N64
2: Dualshock 2
3: SNES
4: GC
5: Dualshock 1

1: Xbox 360 controller
2: Wii-mote
3: SNES controller
4: N64 controller
5: Dualshock 2

1. SNES
2. Dualshock 2
3. Nintendo 64
4. Xbox 360

Honorary mention: Wii remote, only for the concept and how it changed gaming, the actual controller leaves a lot to be desired (though this will change a bit with Motion+)

1. 360 - the pinnacle of dual analog design
2. NES - brought gaming to a new level; truly indestructible
3. Wiimote - changed everything
4. Dualshock - made the PS for me
5. 6 button Genesis - for the age of fighting games, this controller pwned

My preffered controller is the DS3/DS2/Sixaxis.  I enjoy the lightweight nature of the sixaxis.  The controller however is somewhat discomforting after an hour of play.  The 360 controller is a bit large but it feels great and does not cause the discomfort I experience with the DS3 style controller.  I dislike the trigger(odd location for me) and I strongly dislike the offset analog sticks and dpad.  If the button layout on the 360 controller mirrored the DS3 I would be in heaven.

Probably the most pleasing controller of all time was the 6 button genesis controller.  Comfortable and easy to use.

actually, it's the triggers that get me :P

1.PS1/2/3 Dualshock. D-Pad is best in the business (Tekken requires an accurate and responsive D-Pad )
2.GC Controller.
3.SNES
4. N64

360 controller
Gamecube Controller
Sega Saturn Controller
N64 Controller
Snes Controller

Glad to see someone else recognizes Sega Saturn Controller's greatness. IMO 360 is the best 3D controller, Saturn is the best 2D, and Gamecube is a great all around controller.