Like I said before, when I first started running it really bothered my knees. I figured this may have been due to an old sports related knee injury but my hubby insisted that I was young and it could be fixed. I ended up doing some research and talking to one of the trainers at the gym. The trainer at the gym suggested that many women have this issue due to their Q-angle (the angle from your hips to your knees), wider hips can lead to a greater angle (and I have some wide hips).
A large Q-angle puts more stress on your knees, especially when doing activities such as running, she told me to try to "run like a man," meaning run with your feet under your hips rather than the narrow catwalk-eske hip swinging style. This was actually very difficult and felt odd but it did work a bit.
My own research led me to another possible issue, that my hamstrings were significantly weaker than my quads. I tested this theory using some of the weight machines at they gym and it seemed like it was a possibility (my quads also appear quite large). The problem with weak hamstrings is that the quad will pull on the knee when running and the hamstring provides the resistance to keep the knee in place, or in my case, it doesn't and your knees are moved up and down.
My solution: intensify my hamstring workouts by doing lunge walks with weights (I go until my legs are burning), upping the weight on the leg curl machine and dead lifts. It actually worked, my knee pain is non-existent and the backs of my legs are now a lot less jiggly (bonus!).
picture from Womens Health Magazine