The SNES for me. The foundation by which all modern controllers are built.
The now classic four face buttons, shoulder buttons and nice shape, along with a great D-Pad.
Add a couple of analogue sticks and a couple more shoulder buttons and you have the modern day controller. One of the best things Sony did with the first PlayStation was basically copying the design and then adding to that base.
I would have loved for Nintendo to have done the same with the Nintendo 64. I do think the N64 controller worked perfectly well for games designed around it but not always as well with those that weren't. The design also wasn't well suited to future controller developments and gaming requirements.
Imagine the N64 controller had been this instead....