I used to have knee problems. When I started running a lot in HS, my knees would pop out. Over the past 8 years they've probably popped 10 times or so, which is really bad, and is extremely painful as i have to pop it back in.
I ended up, last year, going to the doctor and they ran a battery of physical tests and did an Xray (although I'm skeptical of the need to do that, but they have to do it). The doctor said that he thinks I just need to do knee exercises. He reccomended PT, but I never went because of distance (can't drive 2 hours to go there...and FWIW I live in a different location then where my insurance allows me to go...long story). So I went around and started a lot of squats....that helped, somewhat.
Now my Quads have always been really big and strong because of so much running and wrestling. But my Hamstrings were much weaker; I was worried that things might be out of balance, so i started to do Hamstring exerscises. I didn't do anything fancy - I just did a simple machine (which probably isn't the best option because it isolates the muscle as opposed to allow it to work in unison with other muscles as a group) and I noticed the improvement VERY quickly. I feel much more stable than before. Now I just incorporate anything into a routine, and do a lot more squats...but I needed that 2 months of hamstring exercises to at least bring things back into balance. This is all probably unsubstantiated, but it may help you.