I've been running in shoes since August 2009. I am now considering barefoot/minimalist running. Currently I have a knee issue that I'm recovering from and I plan on starting to transition into barefoot/minimalist running once my knee feels 100%.
FWIW, and I am far from an expert, the knee pain I felt from shod running disappeared quickly after I switched to minimalist. Having said that, I did not transition by going barefoot first, as Jason recommends, and regret it now. (I hadn't found this site yet, nor had I read KenBob's advice either). I developed achilles tendinitis, probably from transitioning and increasing my mileage too quickly. Once the snow is gone and it's somewhat warmer here in Michigan, I will do full barefoot, ramp up gradually and hope that my achilles does not bother me anymore.
Also, I will say that the tendinitis I have dealt with the past couple months is nothing compared to the sore knees and back I had as a shod runner. Then, I always felt I was doing lasting damage to my body, whereas I now feel all I have is an injury that will heal.