"People start fucking there knees up when they go below parallel,it takes a lot of the constant tension of the working muscle also,but I'm also guilty of this,but usually anything below parallel starts digging into the tendon...ouch"
On a squat stopping at parallel puts more stress on the knee than going rock bottom. I could understand the whole 90 degree thing when you are talking about open chain quad excercises like leg extensions, as an extreme ROM will further magnify the sheer force on the knee. On squats though you are not just working quads, but also hamstrings and glutes. While the leverage advantage shifts away from the quads towards the bottom position, at that point the hamstrings and glutes take up the slack. The point at which you reverse at the bottom is a powerful position for the glutes and hams....reversing at parallel will place alot of stress right at the point at which your quad already has poor leverage but the other muscles can't fully compensate.
also I don't quit get what you mean by "digging into tendon"? maybe you have iotibial band syndrome, which can be caused by muscle imbalance between the legs or poor flexibility?