I think this infographic (from SmoothFitness.com) does a pretty good job of identifying the major injuries that runners could potentially encounter. I know that personally I have experienced the patellofemoral pain syndrome as well as hamstring strains, but the runners knee was definitely the most aggravating. I attribute my specific case to excessive heel striking, and overuse due to running more than my body was prepared to handle at the time.
The graphic provides a handy list of ways to avoid these injuries, though I would qualify the specific item referencing “wearing the right shoes” to suggest wearing shoes with minimal: cushioning, arch support, restrictive upper, and heel padding. If you can reduce the influence of any or all of those factors, I believe your shoes will allow your feet to actually do what they were engineered for in the first place.
You would also do well to check out my friend Jason Fitzgerald’s website, StrengthRunning.com. He is my go-to guy for insight into running injuries, and for developing training programs to reach peak performance on race day.