While I absolutely agree the squat is probably the BEST compound exercise overall, using a near perfect form is the key to enhancing muscular development while preventing MS injuries
Consequently I would not recommend an "ass to grass" extreme many are referring to, in all BUT the most experienced BB!
From an anatomical perspective femur displacement below 90 degrees (+ or - 10 degrees) movement places undue stress on the menisci with a disproportionate improvement on muscular development.
Oh I know some swear by such extremes maneuvers but hyperextension or flexion of essentially any joint may actually weaken joint integrity bc the peri-articular structures (tendons, ligaments, fascia) are what's being "stretched".
So when do these injuries occur? Once a joints ROM limits have been reached (when joint stressors have peaked) and actin and myosin overlap are minimal, the lifter realizing he cant's make the lift uses "compensatory" body mechanics and shifts the weight to one side, placing severe stress on an isolated portion of a specific joint. The end result, something "gives".
Now don't get me wrong mates, even though A-G squats can indeed be beneficial, the risk benefit ratio increases so remarkably that form, technique, and overall body mechanics become even more important to diminish the frequency of injuries.
Finally, if your the type of mate that has "bad knees' it goes wo saying any squat below horizontal is asking for trouble, IME