For years I suffered knee pain on and off and I did icing/heat and tried treating the inflammation in various ways. After reading a article by one of my favorite strength coach's, I realized the cause of my knee pain is not at the knee but my tight right ankle. I sprained my ankle severely a few years back and ever since it has been stiff. I realized my knee was over compensating during squats and various movements to make up for the range of motion lost in my ankle. I did not have sufficient amount of dorsiflexion and this is something that helped my knee pain. Having the the right range of motion is very important to avoid running in these issues. Check out a cool ankle mobility exercise by "Movement as medicine".