Recent studies suggest humans running barefoot isn't crazy at all and causes less jarring to the joints than running in sneakers. Less jarring equates to fewer injuries.
Without shoes, runners tend to come down on the balls of their feet instead of their heels as with sneakers. Three videos below from the Harvard University Skeletal Biology Lab graphically show the jarring effect of the heel striking the ground (note the transients in the two heel strike videos).
Harvard researchers maintain that running barefoot promotes a forefoot and midfoot strike, the scientific terms for landing on the balls or the middle of the foot.
"Many people think modern running shoes are necessary in order to run safely and comfortably, but they were invented only in the 1970s. Before then, running shoes were just simple running flats that had little cushioning, no arch support, and no built-up heel. Humans were running for millions of years, apparently safely, in running flats, in thin sandals or mocassins, or in no shoes at all. Our research indicates that they may have been able to do so by forefoot or midfoot striking," according to the Harvard researchers.
For the intrepid who might try running barefoot, but want to build up the requisite callouses on the balls of their feet, there is a half step so to speak. After all, who wants to freeze they're feet off or painfully crunch them on acorns (Fall, 2009 was a banner season for acorns here in the Northeast).
Vibram Five Fingers has a barefoot running shoe that closely mimics running barefoot. They're from the same Vibram folks who've been making rubber soles for hiking boots since 1935.
Vibram based in Concord, Mass. in part funded the Harvard's research, which carries a legal disclaimer that the information it provides is not a substitute for a foot physician's advice. The company tries to appeal to your recollection of going barefoot as a kid instead of trying to get too scientific.
"Now you can experience that same physical and visceral sensation in Vibram FiveFingers—the only footwear to offer the exhilarating joy of going barefoot with the protection and sure-footed grip of a Vibram® sole," extols Vibram.
They look ideal for kayaking on just mucking around on rocks, but they're expensive. On Amazon, the mens go for between $140-$160 a pair. A womens model starts at $80. I would not buy a pair without trying them on first and they're not widely distributed yet. The nearest retailer store for me is more than 25 miles away.
As for running shoes, they may be new in the continuum of time, but constitute a huge industry. Nike isn't fighting back yet - a search of "running barefoot" at Nike.com yielded the following result: "Sorry, we found no product matches for your search."