I too have a thigh chafing problem in those little "marathon" shorts, so I wear Lycra shorts instead - I like the Nike Drifit ones. I find I can wear the little shorts if I wear plenty of vaseline too, but it seems easier to stuff them at the back of the drawer and wear other stuff instead.
A long term solution to the problem would seem to be to reshape my thighs so they didn't rub together. Anyone know any good exercises for that, or do I need surgery?!