When I first started barbell training I did everything according to Rippetoe's suggestions in Starting Strength and Practical Programming (and pretty much still do). He made some very convincing points about why low bar squatting is superior to high bar, and I've had good results using low bar squats.
Over the course of my training however, I've grown to view the low bar squat as more of a cheat and think high bar and front squats are more effective exercises for leg development. When you first switch from a high bar to a low bar squat you can immediately add a significant amount of weight due to the reduced range of motion and increased back and hip involvement. If I had to do
one exercise, and
one exercise only it would be the low bar squat. However, when part of a complete program including deadlifts and power cleans, I think ass to grass high bar and front squats develop greater vertical force production. I
feel like they are 'safer', too, but this is purely anecdotal as I've developed quadriceps tendinitis and some lower back issues from low bar squats, but have yet to experience any problems with front squats.
I also think depending on anthropometry an individual may or may not be ideally suited for one particular style of squatting. If you already have long femurs and a short torso, the additional forward lean the low bar squat requires puts more stress on the spine (you could argue compressive vs shearing force, etc).
This is all just opinion, preference and anecdote, so take it with a grain of salt.
