Full Range of Motion for the style of Squat you are using. Don't do partial motion squats.
originally prepared and posted by Arioch and Spatts at elitefitness.com:
"There are several schools of thought on squat depth. Many misinformed individuals caution against squatting below parallel, stating that this is hazardous to the knees. Nothing could be further from the truth. (2) Stopping at or above parallel places direct stress on the knees, whereas a deep squat will transfer the load to the hips,(3) which are capable of handling a greater amount of force than the knees should ever be exposed to. Studies have shown that the squat produces lower peak tibeo-femoral(stress at the knee joint) compressive force than both the leg press and the leg extension.(4) For functional strength, one should descend as deeply as possible, and under control. (yes, certain individuals can squat in a ballistic manner, but they are the exception rather than the rule). The further a lifter descends, the more the hamstrings are recruited, and proper squatting displays nearly twice the hamstring involvement of the leg press or leg extension. (5,6) and as one of the functions of the hamstring is to protect the patella tendon (the primary tendon involved in knee extension) during knee extension through a concurrent firing process, the greatest degree of hamstring recruitment should provide the greatest degree of protection to the knee joint. (7) When one is a powerlifter, the top surface of the legs at the hip joint must descend to a point below the top surface of the legs at the knee joint."