I recently started running 5-6 miles a day and my knees were getting really sore. My knees were even sore when I was just walking. But I noticed that they weren't nearly as sore when I would walk barefoot. I started doing some research and found out that running barefoot is much better for your knees and your whole body. There is far less concussion on your knees and the rest of your body when you run barefoot. Here is an article about it at Web MD:
http://www.webmd.com/fitness-exercis...ealth-benefits
Anyway, you don't have to literally run barefoot. They have barefoot shoes. Here is what I started using and it has made all the difference in the world. My pain is totally gone.
http://www.vibramfivefingers.com/pro...s_footwear.cfm
For any of you that feel that you can't run because you get too sore, I highly recommend that you try barefoot shoes.