From a design stand point: Easily the Dual Shock in it's various forms. Around for fourteen or so years with only minor revisions. It works ergonomically and it has good brand recognition. To measure it's sucess as a design you only have to look at how other manufacturers change the layout completely every generation, sometime more than once per generation.
If their designs are so great why do they need to be binned every five years? More pertinently, two sticks, four shoulder button, face button, d-pad has become the standard controller layout, even Nintendo use it with the Wii Classic Pro. Although where the sticks go seems up for debate, it doesn't make a huge practical difference. Sony got it abnormally right with the Dual shock, although big handed mooks like me do have to learn to hold it properly or you get achy fingers.
From a usage perspective: Wavebird. Pick up a 360 wireless controller and there's a lot of shaping cues going on from the Wavebird, which is a good thing. Nice shape for your hands, one of the first practical (and reliable) wireless controllers. I pick it over the 360 because I preferred the Cube's button layout, the big green mash-matic A button was a winner. Although the Z placement was daft.
Close second is the 360 wireless, it's profile is pretty similar to a Wavebird, but the button layout is more normal (also it has a more stylish visual design, in as far as a console controller can be stylish). I prefer the four shoulder buttons, but don't like the face buttons and d-pad as much.