I actually think about controllers a lot, so I have way too much to say on the subject! Let us begin.
Notes: I am including the Gamecube controller because it is the best modern style "hardcore" gaming controller Nintendo has produced and it did a few things really well. I am also going to include the "best ever" in each category and any thing I feel is important to mention.
Individual components:
left hand analog stick: N64 > Gamecube >> X360 > PS3
D-Pad - DS > PS3 >> X360 >>>> game cube
right hand buttons: Gamecube > PS3 > Xbox (gamecube was best ever)
shoulder buttons/ L1 and R1/ Z: PS3 > X360 > Gamecube
Triggers/ L2 and R2: N64 > Gamecube > X360 > PS3 (the z trigger was really good, but at the expense of the rest of the controller)
center buttons (start, select, etc) PS3 > gamecube > X360 (PS3 gets best ever)
Qualitative judgments:
Ease of use (beginner): Touch controls > Super Nintendo > motion controls > Gamecube > X360 > PS3 >>> Keyboard and mouse
Ease of use (amateur): X360 > PS3 > Gamecube > Keyboard and Mouse = touch controls >>> Motion controls
Ease of use (expert): PS3 > X360 > Gamecube > Keyboard and Mouse > touch controls >>> Motion controls
Versatility: Keyboard and Mouse > PS3 > X360 > Gamecube
Comfort: Wiimote+nunchuck (minor motion controls only) > Gamecube > X360 > PS3 >> NES
Inherent Fun: Motion Controls > touch controls > controllers >> keyboard and mouse
Best overall: Keyboard and Mouse = PS3 = touch controls > X360 > Gamecube > motion controls
What controller is best all depends on what you are more likely to need. In first person shooters where precision strafing and trigger responsiveness is all important then the X360 works best. The same is true of twin stick shooters. However, in bullet hell shooters (or any similar) the PS3 is easily better because the d-pad and face buttons are better. Same for 2D platformers, racing games, fighting games, etc. Generally speaking, if the analog sticks and triggers are vital to the core gameplay then the X360 is slightly better. For everything else the PS3 is better. However, most games for which the X360 is best a keyboard and mouse is even better.
Note: If a game requires a high precision left stick and good face buttons (3D platformers mainly) then the Gamecube is the best.
It is worth noting that there is no true best control scheme. The 4 big categories all have their own strengths and weaknesses. Keyboard and mouse are best when the precision of a mouse or the versatility of a keyboard is needed. Touch controls are really nice for simple games. Controllers are really good when responsiveness is important. Even motion controls can be really fun if use correctly (Mario Kart Wii!)