Vaseline works if your thighs rub together. Also less material on your legs helps.
I highly recommend these running shorts. Half marathons with no problem. They're dirt cheap, they're airy and light, they keep your junk in place, and they're used by everybody who knows how to run in the military, including all those cats at SOCOM. And these shorts have an NSN. Hah.
http://www.soffe.com/webapp/wcs/stor...egory_rn=14268