I have some (mild, at this point) knee pain. I had a pro-fit done and that made a huge difference... but I still feel that my knee is a bit "tweaked" at times. However, I have found that it responds to very subtle changes in posture. When it hurts, I tend to tense up all the way through my core and up to my shoulders and this just makes things worse. Relaxing my arms/shoulders while ever so slightly flattening out my back causes the knee pain to disappear instantly.

Counter-intuitively, riding harder/faster has a similar effect of stopping the knee pain. I think that when I ride hard, my body naturally adopts a more aggressive position that is good for my knee. Also, I end up using more/different leg muscles which also clears up the knee pain.