The problem with questions like this is that we can't see what's wrong with your knees. There are exercises that will increase the stability of your knees but, depending on what's wrong, could just as easily cause more damage. A better idea is talk to your doctor or a physiotherapist and find out how best to address your situation.
An example of what I mean is this study: http://www.lookgreatnaked.com/articles/ ... _depth.pdf
The greatest risk for injury during deep squatting would theoretically be to the menisci and articular cartilage
Deep squats may also increase susceptibility to patellofemoral degeneration
On the other hand,
ACL and PCL forces have been shown to diminish at higher degrees of knee flexion.
there is some evidence that those who perform deep squats have increased stability of the knee joint