I cut out squats a couple months ago, but that's because my left knee was hurting from it. I'm going to see my orthopaedist this week for a 6-month follow-up of my ankle injury from September, and I'm going to have him look at my knee as well.
I miss doing squats!! Once I can squat again, I'm going to ease back into it for a month or two, then try the 20-rep squat workout!
If squats are hurting your knees it is a form problem more than likely. I have had orthoscopic surgery on both my knees to repair tears from sports injuries and I still squat heavy 3x a week.
The 3 biggest form flaws that lead to knee pain with squats are foot placement, starting the movement at the knee instead of the hip, and stopping above parrallel.
Check you feet placement first. Feet should be shoulder width apart pointing outward at a 30degree angle. When you squat below parrallel your knees should move out to clear room for your torso. This puts you knees pointing out at an angle. You want your toes to point in the same direction as your knees. If your knees are at an angle and your feet are straight this puts a twist in your knee ligaments and leads to pain.
You also want to make sure you are initiating the lift by pushing your hips back and not by bending at the knees. This keeps the knees from moving out in front of your toes and limits the shear force on the knee. To see if your knees are coming forward you can stand in front of a wall with your toes against the wall, arms hanging down in front of you, now squat down. If you cant make it down with out your knees hitting the wall and pushing you back you are moving at the knee and not the hip. Imagine yourself setting back on a toilet, that is esstentially the squat movement. It takes some practice but try it and you will see what I am talking about.
The most obvious thing to check is are you going below parallel. Stopping above parallel shifts the shear force of the lift from the hips to the knee. The knee joint is strongest at it contracted position (below parallel) and weakest at the points in between. When you stop short of parallel you are not only cutting yourself short on range of motion and fiber recruitment but also introducing an enormous amount of unnatural force on the knee.
Check these and see if it doesnt help.