I read several articles on this in Men's Health, Outdoor and BACKPACKER magazines sometime ago and I had to go back and get the details but the arguments for bare footing look convincing enough.
The Tarahumara tribe in Mexico is known for their endurance in running but even more so for how old they can be and still truck it. This hippy runner guy ,Caballo Blanco, lived among them and became a huge disciple of barefoot running. He then trained Christopher McDougall... who contributed the articles I remembered.
They argue that comfortable running shoes are the biggest contributor to injuries. As shoe technology becomes more and more comfortable, there appears to be a rise in injuries. The thought it that they cause a person to run at an unnatural longer stride and this leads to increased impact on joints. Barefoot running acts as a governor. You can only run so hard without shoes and it forces you to run at a stride that is natural for your body.
I have a co-worker that has started running in vibram five fingers and he swears by them now. One of the guys at REI that I talk with has started backpacking in those same shoes. (A similar argument for lighter shoes, getting away from mega-boots, is getting popular among backpackers)
