I've done both.........all the way down and just a little shy of parallel. I rarely see anyone in my gym go anything even close to parallel. They are more concerned with how much weight is on the bar than how much they can actually move even a little...i.e. EGO!
You definitely need a certain minimum range of motion to get the maximum benefit from squats. What that minimum is, I'm not sure. I generally start to go shy of parallel as the weight gets heavier on my last couple of sets.....not on purpose.
Aside from the depth of the squat, the biggest mistake I see is leading with the hips instead of the knees. To say it another way, you see a lot of folding at the waist....more of a "power squat". Bodybuilders are more concerned with accomplishing what they call an "olympic squat"...it will build more muscle in the legs