i see the mention of box squats a couple times in here so i'm gonna give you my opinion on them...........
box squats only work if you use them the way they are intended. sit on the box and stop all momentum then explode off the box with all you got. many times what i see from guy's doin box squats is they let the knee push forward out on the toe and never break parallel by the time they hit the box. so they do a tap and go but never really to depth. any one can prevent themselves from breaking parallel by simply letting the knees go forward rather than forcing them out like stated by BTB.
The thing with breaking parallel is it will incorporate more muscle the deeper you go. If anyone is a nonbeliever of this i challenge you to seriously do some ATG sessions and tell me you aren't more sore doin that then a typical BBer 1/2 squat which will really only benefit you if you move mountains and you use AAS. If you have trouble getting deep into the squat than simply lower the weight. Slightly point the toes out, force the knees out not forward, keep the back arched and focus your head up and not forward. Start with the bar only if you have to but if big Steve can put his ass on the ground when he squats anyone can. He is a big man move'n piles of weight and i have never seen him squat once above parallel.