I'm not a huge fan of controllers, but between the two... definitely the X-Box 360. I might be biased as I own an X-Box (though I haven't used it in close to four years; it red-ringed and I never bothered to get it fixed), but while I was at university two of my roommates had PS3s and I got to spend a lot of time playing that system as well.
I found that the PS3 controller had the same issue that the PS2 controller, and before that the PS1 controller, had with me - after an hour or so it gives my hands really bad cramps. I don't know if it's the shape or the button layout or what... but Sony's controllers have always been extremely uncomfortable in my hands. The X-Box controller has never had that problem with me (although the original controller for the first X-Box, the freaking huge one, was admittedly pretty uncomfortable for me as well).