From a mobility and dysfunction standpoint we could look at the joints over and under the knees: Ankles and hip.
There are a couple of things that can cause knees collapsing in:
1) Flat feet. Or something similar to it. The point lies behind your weight distribution. You put too much weight on the medial side of your foot, which causes the arch on your foot to lower and vanish. Now this can lead to some knee issues because when your have more weight on the medial side of the foot, your tibia and ankle are also more easily collapsing inward. Anthony Mychal suggested an exercise where you would squat down, then lift your toes up, and then move your weight around your foot, try to find a proper tripod balance on your feet. That's one way to notice how your foot balance will affect on your knees.
2) Firing issues or weakness in the abductors and stabilizers. The glutes (Especially glute medius), TFL, vastus lateralis. These are all muscles that try to drive your knees out and femur to abduct. If they are not working right, the adductors will have more control, the knee will be less balanced. Solution? Try to get some activation on the muscles. Stu threw a couple of great exercises, like the band on your knees. You can also do sideways walking with the bands to get those adductors going. Then for glute medius there is the side clams and lying lateral leg raises (also great for the TFL). On the latter ones you might want to try to get the glute medius more involved by pressing the lifting legs heel to the wall (Extending the hip).
3) Tightness. Soft tissue work just about everywhere around the knee is preferrable. Maybe some dynamic stretches. Especially on the adductors. Try this exercise by eric cressey: http://www.youtube.com/watch?v=f4HMlyaH ... ults_video
These are some ideas that came to my mind. It could be any of these, or just poor motor control, flexibility issues, anything. It's hard to say from such little information, but I'd recommend to try some of this stuff out.