There's been some really good discussion going on in this thread.
One thing I want to point out is the point SRS makes:
I tend to miss my squats right at the bottom, and I definitely found this to be the case. Furthermore, when I switched from box squats back to free-weight squats, I had a lot of issues with my adductors. I attribute this mostly to the fact that box squats don't require any "stabilization" and the reversal of direction is broken by sitting on a box.
With that in mind, Jakerz brings up a good idea about using the box to keep the form tight and hit a constant depth. I think I might give that a try.