I used to run barefoot on the dreadmill. This is before I knew the worth of good running shoes. My knees killed me afterward every time.

When I was in FL this fall I ran about three miles barefoot on the beach. (Pictures of my blisters are on my blog.) One of the best runs of my life and the softer surface didn't cause any knee pain.

My husband uses the Vibram five fingers & loves them. Especially for trail running where it's nice to be able to use your toes to help grip the ground. I plan to try them this spring, but for now am just getting used to toe socks.

I'm sure it's just one of those things your body can adapt to. To me it's worth trying, but I'm guessing it will take time to build up calluses and proper form.