There's a growing subculture of athletes, mostly long-distance runners, who are starting to turn away from fancy training footwear. "Born to Run" by Christopher McDougall is probably the most popular piece of literature on the subject.
I'm totally on board. From an evolutionary standpoint, it makes no sense to strap a 2-inch rubber heel to your perfectly functional foot. Barefoot runners tend to land on the forefoot, in a position that allows the calf muscle to get involved and absorb the stress of impact. Athletes with elevated, cushioned heels tend to land on their heels. In this case, the muscles of the lower leg and ankle are not involved in minimizing the impact force on joints.
Take a look at these two comparative videos. I feel this is pretty strong evidence supporting the idea that wearing elevated-heel shoes inhibits us from achieving our natural motion:
Forefoot striking vs. Heel Striking
Note that both runners are barefoot, even though runners who have learned to run barefoot generally tend to strike with the forefoot. Heel-striking with a cushioned sole looks like this.
I'm aware of one study that analyzed the torque experienced by different joints in shoe-clad and barefoot runners. This study found reduced torque in the hips, knees, and ankles of the barefoot group. Unfortunately, only the abstract seems to be available for free.
Since our culture demands footwear for most occasions, I'd recommend a couple of options:
These are my personal choice. I work, train, and walk around in these. The toes are separated, and the sole is super thin. I've had one pair for over 6 months, and they are still in fantastic shape. I think part of this has to do with the fact that I walk more carefully when I wear these. At just shy of 200 lbs, I find myself accidentally sneaking up on people occasionally because my feet contact the ground fairly softly. They feel good, but it's still not the same as being barefoot.
I should mention, however, that these shoes are terrible in the mud and really start to stink after a while. They are washing machine-friendly, though.
-Terra Plana VivoBarefoot These look great, but I haven't given them a try yet. The Vibrams are quite a fashion statement, and the TPVB's offer a more subtle alternative (at a much higher price).
I'm not affiliated with either of these companies. There might be some other good alternatives out there as well of which I am unaware.
Finally, a word of caution: As with a lot of the subjects I discuss, there is a definite transition period from the cultural norm (wearing elevated heels) to the functional (barefoot). Your calf muscles and Achilles tendon need a little time to build up and adjust to their larger role of cushioning initial impact. If you're going to try barefoot training, start with shorter distances and durations.
Running Before the Modern Shoe