Foam roll your quads (can be very painful at first), standing quad stretch after each squat session and at least once a day, low bar squat (less stressful on the knees than high bar or front squat), video tape yourself to be sure you are going to parallel (otherwise your hamstrings aren't balancing the force from your quads and your knees are stressed), be sure that your knees don't track forward at the bottom of the squat (stressful on the knees since you are removing tension on the hamstrings, see Rippetoe's terribly useful block of wood), knee wraps or knee sleeves can be helpful.
Squatting correctly is more nuanced that it would first appear. Starting Strength 3rd edition explains the mechanics of the squat in great detail and justifies why you should squat in a certain way.
Not everyone can squat but most people are just doing it wrong. It is such a useful exercise that you should be very sure that you actually can't before you give it up.
You can get good critique of your form by posting a video at the starting strength forums where you might also find useful information from a search for patellar tendonitis/tendinitis.