I recently went through something similar. My left knee started giving me problems right after Christmas. It mainly hurt when running, but then it started to give me some pain when cycling (both road bike and mountain bike). I went through three pairs of running shoes thinking that had something to do with it. I tried running more, and I tried resting more, but neither helped. Finally, I consulted with a local pharmacist and he suggested I try glucosamine (1500 mg tablets). He said sometimes cartiledge in your knees gets damaged and can form a sharp point which will irritate the joint. Glucosamine is supposed to help smooth it out again. It took about 3-4 weeks to do the trick (the pharmacist told me to expect that), and the first couple of days it really upset my stomach, but my body got used to it. Might be worth a shot. It was a big help to me.