Short summary: in the early 60s, there was some research suggesting that squatting past 90 degrees was bad for the knee ligaments. This has subsequently been disproved, with indications being that unless you have pre-existing knee damage, squatting full depth is okay (and it engages muscles that don't get fully involved if you stop higher up).
Note: I am not a doctor or trainer and do not play one on the internet, and I am a strong believer in finding out what works for your body in practice, and if something hurts, not doing it.
But having read the info that's out there: I squat below parallel, as low as I can go with good form (no back rounding or knock-knees, etc.). I do have a history of knee problems, and squats have never aggravated my knees.
no subject
http://www.stumptuous.com/learning-the-squat-1-debunking-the-myths
http://ask.metafilter.com/129091/Are-full-squats-bad-for-the-knees (extensive argumention)
http://www.acsm.org/AM/Template.cfm?Section=current_comments1&Template=/CM/ContentDisplay.cfm&ContentID=8652 (the American College of Sports Medicine summarizes research and recs going to where the tops of your thighs are parallel to the ground)
http://www.apec-s.com/Deep%20Squats.pdf
http://gubernatrix.co.uk/2008/11/how-low-should-i-squat/
Short summary: in the early 60s, there was some research suggesting that squatting past 90 degrees was bad for the knee ligaments. This has subsequently been disproved, with indications being that unless you have pre-existing knee damage, squatting full depth is okay (and it engages muscles that don't get fully involved if you stop higher up).
Note: I am not a doctor or trainer and do not play one on the internet, and I am a strong believer in finding out what works for your body in practice, and if something hurts, not doing it.
But having read the info that's out there: I squat below parallel, as low as I can go with good form (no back rounding or knock-knees, etc.). I do have a history of knee problems, and squats have never aggravated my knees.