This brings up something that came to mind immediately after getting an Xbox... the controllers are in the ideal configuration for most games. Think about it. Most (all?) modern games use the analog stick. On the Gamecube and Xbox, the analog stick is in the primary position with the d-pad relegated to the lower area out of the way. For some reason, Sony has decided to stick with their d-pad in the main position. When switching back to the PS2 after selling my Xbox, it took some getting used to. It felt awkward to have to position my hand so low on the controller to use the left analog stick. I remember wishing they were reversed like the others.
I agree that the Playstation controllers are very comfortable and I really don't even notice anything out of the ordinary now. I especially like the 4 shoulder buttons as opposed to the 2 every other console has had. It is something interesting to think about, though. Will Sony cave in and change the PS3 controller?