Hi Cory, I have been dealing with knee pain from running and other sports for many years. It got very bad in high school and its still with me now, but much more manageable. If you have the means to see an osteopath and/or physical therapist, I highly reccomend that you do so. Here's what helped me the most: Get really good insoles for your running shoes, and maybe all your other shoes too. If you have the means, getcustom insoles made to you foot shape. If not, 'superfeet' makes good ones, but make sure you get the right ones for you arch support needs. Also, STRETCHING. When I started a stretch regimine in physical therapy it was the first thing that really made a difference. It is difficult at first but it pays off and then keep up with it. There are also exersizes that a physical therapist can recomend. Ice is a really good way to relieve pain without drugs. Don't do heavy weightlifting like squats without medical advice but you can do leg lifts with light ankle weights. Here are some examples.
http://www.bigkneepain.com/knee-exercises.html
(at the bottom is a list of stretches. It is very important to stretch AFTER leg strength excersizes and RIGHT AFTER running)
My osteopath changed my life. If you live near washington, dc, go to him:
http://www.quistmd.com/index.html
If not you can find a physical therapist who does the same 'active icolated stretching' (its crazy awesome) in your state:
http://www.stretchingusa.com/aistherapists.cfm
After stretches, the biggest change in my knee pain happened after I went vegan. The reduction in infammation did real miracles. My knee pain is so much more managable now.
Good Luck!