Not going lower than parallel is an old rule of thought that has little proof. In all honesty, mecahnically, you knee is at the worst stress when it is at 90 degrees, as the moment arm on the femur is the longest.
Anything deeper than that and the moment arm (perpendicular distance between the center of mass and the axis of rotation) starts to decrease. ...and in addition, you knee is supposed to bend that way, as long as you do it with the correct posture, you're plenty safe.
As for "don't let your knees go in front of your toes" ... I don't like that either. What good does it do to displace your hips that far behind you and put all of the mass you are trying to lift away from your own connection of force to the groun (i.e. your feet)????
In relating to another post, squatting in a smith machine does nothing for your neural control of your lower body. With the exception of rehabilitating a stroke victim who may be experiencing hemiplegia (paralysis of only one side of the body), why not teach someone how to balance?
The take home message, we should not be curtailing a workout away from the full range of motion, this causes us to get away from working the joint the real way it's supposed to work.
Hopefully someone agrees with me on this one...
I completely agree with you, what is the deal with all this Squat bashing? There is no better exercise, especially if you work it through the full range of motion. I haven't heard much about the neural control when doing the smith squat, I assume you mean that it is not as beneficial for the training of the CNS. It does have its perks though, since you are able to place your feet slightly ahead of the weight and have better posture, the smith machine is very good at isolating the knee extensors (All 4 quadriceps muscles). However that does mean the hip extensors don't get much work. I think varying your workouts by including both the squat, smith squat, and maybe the front squat as well is great for building power in the legs.