Having been subjected only to Perfect Dark/Goldeneye for the n64, Halo for the XBox, and Rainbow Six for the PC, I'd say the n64 controller.
Dual Analog Stick Style
Mouse Style
Touch Screen? Should that even be included?
Keyboard Keys. 
That other option that you forgot, you fool!
Mouse/Keyboard combo
Having been subjected only to Perfect Dark/Goldeneye for the n64, Halo for the XBox, and Rainbow Six for the PC, I'd say the n64 controller.
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