The Canadian Medical Association Journal recently published two articles about barefoot running. The articles look at both sides of the issues and basically conclude that there is no research currently available that says running with high-heeled cushioned shoes or running with a barefoot style is beneficial or detrimental and agree that more research is needed.
Here are the articles (with links):
The rise of barefoot running
Low-tech running shoes in high demand
My favorite quote out of the two articles is one by Dr. Daniel Lieberman, "The key thing is not being barefoot, but using a barefoot style, and not colliding into the ground with your heels.”