I had been running for a few years in "motion control" shoes before I tried going barefoot. I'd gone to a local running shop, they watched me (and videotaped me!) on a treadmill and told me which shoes to get. Over a couple of years, I kept having different issues- IT band pain, patello-femoral tendonitis (went to a PT for that one), shin pain, and at one point, I went to a podiatrist because of a re-occurring bruise under my big toe. He gave me some temporary insoles and wanted me to try them before I came back for orthotics. The insoles made my feet hurt so badly after 1 run that I just had to stop running for several weeks. Then I got really hooked on cycling and didn't run for a year or more.
When I started running again last fall, I started having shin pain again. When I started researching the causes, I happened upon some barefoot sites. I was pretty skeptical, but tried it anyway. I mix it up between barefoot and using the Vibram shoes (depending on where I'm running). My feet hurt at first, but it was more of a muscular-type pain (like I'd been lifting weights w/ my feet

) that went away after a day or two. Now, my left foot (which was flat) now has an arch, and I ran a 50k about a month ago without a hint of tendinitis!
Oh yeah- and when I DO wear shoes, it's a Vasque Velocity, which is actually a pretty chunky shoe, but I like it because of the fit and the stone shield in the sole (some of the trails I go to in Arkansas are pretty rocky)