XB Elite, followed by the regular 360/xbone/xsx controllers (they're all basically the same thing). From there I'd go DS4, DS3, and beyond that I don't have much opinion. I will say that the Gamecube and N64 controllers are among my least favorite modern controllers.
I think that XB, since they moved past the Duke, has the best controller by a wide margin. But, I think a lot of this is just about what one gets used to. I game on every system, but tend to lean towards Xbox because I prefer that controller for shooters, and I play a lot of shooters. Consequently, that controller feels most comfortable to me. Also, the slow pace of evolution of the controller helps it feel familiar, I think.