I have been running in Vibram KSOs for a little over a year and a half now with excellent results. No significant foot, ankle, knee, hip, or lower back pain. Granted, I don't run very far and I limit myself to three or four days a week max. My goal in this coming year, I hope, is to increase both my mileage and frequency. Either of these goals have proven problematic in past years, primarily due to the various pains mentioned above. But I have discovered that I can, in fact, run relatively pain free on a regular basis.
Just this morning I ventured out into a dark, cold 26-degree morning. Now you northern folks may think 26 degrees is a spring day, but to this native Houstonian it's nothing less than an arctic blast. I've been eager to break in (although they don't need it) my newest pair of Vibram running shoes -- the Bikila. A run under such conditions would normally cause me to stiffen or cramp up at the very least, or bring on a tightening of ligaments and muscles leading to shin splints or any number of joint pains. But to my continued delight, I not only felt great but enjoyed my run. The Bikila model performed flawlessly (as I suspected). It's more than just the shoe, however. It's the move to minimalist running that has transformed my running form this past year and caused my lower legs and feet to strengthen, enabling fewer pains and injuries.
Tired of running in pain? Look into minimalist or barefoot running. You may find it odd at first, but it could very well be a solution to at least some of your running pains. I'm excited to see a whole host of companies coming out with their own particular brands of minimalist running shoes in response to brisk demand, brought on most assuredly by happy runners. Did I just use the word "happy" and "runner" in the same sentence?
Retrain your mind. Think outside the running box. Try something new. And have fun.