Take it from a Harvard Professor... barefoot or minimal-shoe running is the way to go!

From a recent post by Chiggers on the Dragondoor Forum...

Us kettlebell-lifters love to train barefoot, and for good reason. As humans, we have been lifting things in bare feet for at least a million years... in shoes, not so long : ) Our feet are adapted to bear weight the most efficiently the closer we are to barefoot. For those who need orthotics to correct misalignments, the most minimal and thin-soled shoe that will still support the insert is recommended (think converse Chuck Taylors). Why would running be any different? Humans have also been running barefoot a lot longer than in the thick-heeled running shoes invented in the 1970s!

And now, the science... complete with groovy computer graphics comparing heel-strike vs forefoot-strike:

YouTube text:
Harvard professor Daniel Lieberman has ditched his trainers and started running barefoot. His research shows that barefoot runners, who tend to land on their fore-foot, generate less impact shock than runners in sports shoes who land heel first. This makes barefoot running comfortable and could minimize running-related injuries. Read more here http://www.nature.com/news/2010/10012... and find the original research here: http://dx.doi.org/10.1038/nature08723