The gamepad.

Gonna have to be Dual Shock, specifically the latest model. If only it had the battery life of a DS3 controller it'd be perfect. Well, until the DS5 comes along.

Gen 5 - N64 pad

Gen 6 - DS2

Gen 7 - 360 pad

Gen 8 - DS4

DS4 is the best overal, it just an evolution of all the best controller features added to one controller which no early gamepad before it can match.

For nostalgic reason I'm fond of the Atari joystick and Sega Master square pad.

Wiimote + nunchuck, was perfect for shooters and 3D action games, thanks to the pointer.
The dualshock is perfect for 2D games and fighting games.
The X360 (and Xbox One) controller are confortable for most genres.
The Gamcube controller, is the most ergonomic but the button layot is great for some games and unconfortable for others.

Keyboard and mouse

DualShock 4, followed very close by the Xbox 360 controller

White DualShock 4 by CurtisArzate, on Flickr

My favorite controller is the gamepad. I mean, c'mon... it's got a massive touchscreen, speakers, webcam, gyro motion controls. I see many people basing their decision on how comfortable a controller is. If I were to select the most comfortable, I would say the Wii U pro controller. I haven't tried the new Playstation controller but from what I can see, it looks like a step in the right direction. Previous Playstation contollers are tiny and uncomfortable. Give me the big duke from Xbox over that thing any day.

This for me too but only because I am a big guy and regular controllers forces my hands too close together - making them uncomfortable to hold for longer periods.

I would like the Gamecube button configuration to be more popular: to me it is a very intuitive configuration.

N64, PS4, Wii

N64 - such a unique controller means your gameplay style can change simple on how you hold it..

PS4 - best over all controller probably...in terms of comfort and responsiveness

wii remote - i loved it becasue it can be used so simply (like in rhythm Heaven Fever) or also it can plug into the procontroller for xenoblade, goldeneye, and monster hunter tri.

GameCube/Gamepad.

They're both close to perfection in my mind, it's just the wires that let the gc down, and the batteries for the gamepad. Otherwise they're spot on