I've always loved the N64 controller and it bothered me for a long time that console makers decided to move away from that kind of layout (specifically with the analog sticks moving all the way to the left of the controller). I've seen people hate on it but to me it was perfectly layed out. I haven't held a controller yet that felt as comfortable to me.
360 > DualShock 2 > Gamecube > Dualshock > SNES > NES 64 was ok but a bit funky, Xbox was too bulky, Wii is too niche, Genesis was like SNES but not as good, Dreamcast bulky, Dualshock 3 triggers don't feel right. My fondest childhood game memories are of the SNES controller though.