I think training barefoot is THE way to train. It promotes a proper running posture on the balls of the feet and builds proper muscle structure in the foot and legs. I do as much training barefoot as I can and only use extremely low profile shoes when I have to. I think that it's better to have some type of protection and be able to sustain training rather than destroying your feet in one session and being out for long periods of recovery time.
When I do wear shoes, I've found Inov-8 to have the best shoes on the market for low profile running. They specialize in trail running shoes that have super low profile insoles but still provide moderate protection from the elements and are super grippy. Their 3mm insoles are like a piece of paper under your foot. I feel just about everything I run on in my shoes without being hurt by it. Even their 6mm thicker shoes still promote a proper toe running posture.
I have two pairs (I order them from Zappos.com). The F-LITE 230 PK's (3mm insole) for running, Pakour, olympic lifting and CrossFit type workouts. They are extremely low profile and I feel everything. They also have sticky rubber and great grip. For more hazardous conditions, I use their slightly heavier version with Goretex. The F-LITE 305 PK GTX's (6mm insole). I use them for trail running and other harsh environment training. I posted pictures of both of my pairs.
230's
305's
No matter what type of shoes you wear to run, you should adopt a running style where you land on the balls of your feet (the padded area right behind your toes). This is the proper piston action for your foot and leg. By jamming on your heels every stride, you put extra stress on the shins, calves, knees, thighs and hips, which will also affect your lower back. When you run on the balls of your feet, you develop your facia muscle and you're using the entire foot and leg systems to run, spreading impacts over a more broad range of muscles and joints.
Hope this helps some of you.
Train hard and often.
