no offense, but wtf do crossfit people know? i read that thread, and it was full of fail.
first, people must stop answering with black or white absolute answers, b/c the knees are more complex and there is a lot that isn't well understood.
you have the tibialfemoral interaction on the menisci, the loading of all the ligaments, loading of the quadriceps / patella tendons, and patellafemoral stress. anyone of these things could be considered "knee pain" and all are likely stressed in different kinematic & force combinations.
i'm trying to look over this
review article I found on PubMed. it's pretty long but discusses various consequences to different loadings. in what they discuss it seems most experiments don't go past 90-100 degrees of knee flexion - that doesn't mean going past is bad, however.
in terms of shear stress, yes its true hamstring activation will help reduce stress (referring to crossfit thread), but that is only one element.
as the knee flexes in a squat, there is an increasing patellafemoral force. basically, put a piece of rope over your kneecap, and pull at both ends at different angles. if you pull away horizontally, there won't a force, but as you begin to pull down at more vertical angles, the compressive force will increase. so the compressive force between the patella and femur increase (at least up to 90 degrees flexion).
if the patella is not properly aligned, this can certainly lead to high stress / pain / cartilage degeneration. however, it is not clear if even lower knee angles increase the stress, because the torque demand at the knee may lower in deep positions (relative to 90 degrees).
squats (at variable depths and resistances) are not going to be good for everyone. people have different pre-existing conditions, relative segment lengths (think femur / tibia orientations), and patella mechanics. certain things may stress their knees more. obviously a great indicator is pain. if you are feeling knee pain when doing some time of squat, then stop doing it! if it feels okay, then might be fine to continue with.