Has anyone had bad longer term experiences with these or other "barefoot" shoes?
Rotating your shoes is one of the best ways to prevent injuries if you're trying to move towards more lightweight shoes. I try to use a combination of racing flats, Nike Free 3.0s, and trail flats, and variety really does help cut overuse injuries. If you intend to run fast on trails, you can get many of the benefits(e.g. low weight, flexibility, and a more responsive foot feel) with a trail flat like the inov-8 X-Talon 212, while avoiding a lot of the catastrophic injury possibilities.
One final note: although I love my pair of Five Fingers KSO, they smell really bad very quickly. If you get a slightly larger size, some people have luck using the Injinji toe socks with them.
I'd recommend hand-cleaning them with washing powder in the sink, and really scrubbing the insides of the soles and fabric around the toes.
Did you have any problems?
I started to get a little plantar fasciitis from too much mileage in my racing flats and excessive downhill running, but was able to fix that by rotating my shoes more and sticking to the flats.