Edziu wrote:Well, I know I'm about to get all the rotten fruit thrown at me but let me have my say.

There is a considerable body of opinion that low squats put a lot of stress on the knees. Having said that though, I'm gradually lowering my squat to get more posterior chain involvement. Still, I'm really reluctant to go much lower - Instead I go to just below parallel and do extra glute ham raises to pick up the slack. No problems so far.
OK OK I'm ready for all the stinky rotten fruit now

Here comes the first piece...just kidding. In all seriousness though I think you will find the people that make up that body of opinion do not squat or if they do it is no where near a full squat. Although I have only been doing the stronglift's 5x5 for 6 weeks I have always done squats and deadlifts. You will see it recomended over and over here but reading the Starting Strength book will give you the basic understanding of the body's mechanics and show you why this opinion is flawed. One of the easiest ways you can prove the benefits of full squats is to take measurements, not on your thighs but on the knee itself. As your strength increases so will the muscle mass that supports the knee. More muscle more stability.
I had reconstructive surgery on one of my knees 12 years ago for torn cartillage and a tendon. Even after surgery I continued to have problems with it. After a few months of full squats the problems where almost non-existant. I have been deep squating for over a year above my body weight and closer to 1.5xbw with no pain or stability issues.
If you really want to do something that will reak havoc on the knees try what most do because they believe squats are bad for the knees,leg extensions.