I run in Vibram FiveFingers. It's not quite barefoot running but pretty darn close. They do wonders for my knees and ankles. Before I was cutting out because the pounding on my knees were killing me around 2 miles, but with my VFF I can run 5+ miles consistently. It's a whole different ballgame. Running w/ shoes, I struggle to walk the next day. Running with VFF, I feel even more energized the next day.
I know it doesn't work for everyone, but it's worked for me. That's what matters to me of course. Other people have different experiences. But at 6'5" 215lb, the less stress on my knees the better.