it sounds funny at first, but, done properly- deep squats reduce the strain from the knees and puts more stress on your hips, not knees. I don't need 2phd's just to know this one little fact. Parrallel squat takes away strain from the glutes, deep squat adds strain to the glutes. Parrallel squats adds more strain to the knees, deep squat reduces it.
This is more or less the argument that Rippetoe presents in Starting Strength, if I remember. It's a great book but he didn't persuade me on ATG squats. The most obvious objection that occurred to me is that even if we grant that the parallel position is so lousy, you're still passing through it twice during the ATG ROM.
He also discusses the engagement of various muscles in the deep squat, but never explained to my satisfaction why that would reduce stress on the knee joint, which continues to act as a fulcrum with a particular load regardless of the muscles which are in play on its lever arm. Why would engaging glutes (which engage anyway, but I digress) reduce the load on the knee? I never got that.
(He also talks about tendons balancing shearing forces within the knee in the ATG but, as I mentioned, I was told stresses within the joint rise dramatically as the angle increases past 90, balancing tendons or not).