Yeah, it sounds like you have aggressively pursued using correct form. For most people, form is the issue, but I get the feeling that you might just have a physiological issue with doing squats. Have you tried leg presses as a substitute?

Another possible thing to TRY (if it hurts don't do it) are Goblet Squats. Look up a youtube video and you will quickly see what it is. It is a very effective way of increasing hip mobility so that if/when you do try to do squats again your hip flexors will take the weight instead of your knees.

Also, (this is extremely important), google "low bar squat form." Anyone with knee issues should be doing low bar squats (in fact they are all I do, because they are as good as high bars but easier on the knees). If the bar isn't resting BEHIND the traps and on top of the delts, then you are doing a high bar squat which puts far more stress on the knees.

Look up videos by Rippetoe. He is controversial for advanced lifters, but for beginners he is a good resource. He is also a huge advocate of the low bar squat, and he has a video on Vimeo where he talks for several minutes in detail about positioning the bar for the low bar squat. Get the bar position correct, and the squat will take care of itself.