I think, just in terms of pure digital functionality, it's a tie between the SNES and the Saturn. tc mentioned the 3D controller, and it's good as well, especially for folks that have pretty large hands. I find it very comfortable.
If we're talking current-style systems, my favorite has actually become the 360 pad. The layout is not an issue, I can deal with the Dual Shock or the 360 analog configuration. It's more the feel of the analog. The 360 controllers offer up a bit more resistance, and as such, I'm able to be a lot more precise than with a Dual Shock. The d-pad does suck, but I've gotten used to it, and it's never quite as bad as folks make it out to be. Heck, I've managed to beat SF IV on the highest difficulty with multiple characters with it, mostly without a hitch. I'd prefer better, of course, but it works well enough.