To add to the anecdotal support for barefoot running: I ran in traditional running shoes for years ... and my knees were eventually not happy. I gave up running, assuming I just had bad knees.

When I heard about barefoot running a year or so later, I tried it. Running on the balls of my feet took some re-learning but the knee pain never came back. I continued to run for 4 or 5 years. (I'm not sure why I started walking instead of running — getting older? Or to share the time with my non-running wife?)

(On a tangent: I dislike any kind of shoe-clip when biking. I feel that pulling up on your leg/knee to power a bicycle goes against the design of our knee.)