Wired has a piece up To Run Better, Start by Ditching Your Nikes, which discusses the controversy over the utility of running shoes. Of course the "support" that typical athletic shoes provide is real. when I switch to flip-flops in warm weather it takes a few days to get comfortable walking up or down hills. There is a shift in the emphasis of which tendons you have to work.
I run in downtown Boston. There's enough junk on the ground that it really wouldn't make sense to run without shoes even if it is less efficient. I really would rather my shoe gets a glass fragment than my foot.
The main point of the article is not to run barefoot, it is to run more on the balls of your feet and less on the heels. It argues that heavily cushioned running shoes cause people to run on their heels, which increases the impact. This seems absolutely correct to me.
Thats the purpose of the Vibram 5 fingers mentioned in the article Joshua.
I am Parkour and Strength and Conditioning Coach and athlete. From working with athletes it is incredibly clear to me that more time training barefoot equals better healthier athletes. The foot is the foundation of the body when encased in a shoe it can not develop the strength and dexterity it is built for.
People with week, unco-ordinated feet are far more likely to develop knee, hip and lower back injuries, they are also less able to demonstrate agility, speed, strength and co-ordination.
Shoes are useful for sure, I think of them as performance enhancing equipment I can not get the same traction on many surfaces barefoot as I can with good rubber under my foot. A nice hard cushion under the foot alows me to take larger harsher jumps without worrying about injuring my feet. So I do use shoes but I try to go barefoot or in vibrams or similar low profile shoes as much as possible in life and training.
Men's Health had a pretty good article on the Tarahumara Indians in Mexico here:
This is the tribe that runs 100+ mile races barefoot or nearly barefoot.