My personal fave is probably the gamecube controller - always loved it's shape and design but I will admit it has its flaws. Objectively speaking though I think these are probably the top 5 in terms of function and innovation:
NES - Not a big fan of its shape but the D-pad was such a step up from digital joysticks & dial pads that came before it.
SNES - Epic controller for its time and still brilliant for retro gaming (I use this on my raspberry pi)
PS1 - Dualshock was the first to have twin analog sticks which is necessary for 3D gaming (that and built-in rumble was cool).
360 - Easily the best pad of its generation. PS3 was still stuck on old dualshock design and the Wiimote was...different I guess.
Wii U - Very underrated imo. Gamepad is genuinely comfortable with built in screen allowing user to play without TV (very useful feature in my house!).
EDIT: Thought I should give mention to the Saturn pad. Not really innovative but it is great for retro gaming especially on old school fighters which the Saturn excelled at.
