Hmm, very interesting question...
I first gonna have to go with the Wiimote + nunchuck, one of the best controller setup I have used in the longest time. Easy to use, accurate, relaxing, and when you want to "feel" like you are actually doing something you use motion controls. That is number one for me.
Then comes the keyboard + mouse. I may not be the biggest PC gamer, nor do I game often on the PC. But I definitely preferred playing the Jedi Outcast game, KOTOR 1 and 2, and Oblivion on the PC. It's just easier to get access to all the options you need when playing the game and is accurate with the mouse.
After that it is the Wavebird controller. The first wireless controller for the consoles I believe, its comfortable and easy to use for the Smash bros. game. But its soooo difficult for FPS games (I guess compared to the Wiimote that is). Then comes the DS 2 and the 360 controllers, although they are very very close for third place in my eyes. Very close indeed.
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