I currently have jumper's knee right now. I've stopped playing basketball for like 3 months, and squat lightly only once a week to maintain the strength.
My squat got up to 405x4 but I never deadlifted, so I think part of the reason I got it was through muscle imbalances.
Here's what I'm doing to help myself:
VMO Activation - I'd rather have my VMO fire before the rest of the quad because it stabilizes the patella. This would be safer. If you look at my thread here, I noticed that in my left knee where I have jumper's knee, the VMO doesn't fire clearly before the rest of the quad, where as in my right leg it does:
http://www.adarq.org/forum/strength-power-reactivity-speed-discussion/vmo-firing-patterns-%28video%29/Glute Activation - My quads were very overractive since I never deadlifted. Perhaps my quads are taking over in movements that should be glute-driven, which is putting more strain on my patellar tendon.
Quad Foam Rolling - This will help with the tightness in my quads and help them "relax" more.
Rectus Femoris Stretching - This is the single most effective stretch I've done that helps alleviate the pain in my knee:
http://davidlasnier.com/wp-content/uploads/2010/10/sports-training-rectus-femoris-stretch.jpg^^ Yes, the back leg must be up like that. Otherwise you're just stretching the hip flexors. It will also help combat the overactivity of my quads.
Strengthen Hamstrings - I really have to strengthen the antagonist muscle to my quads to help inhibit the overractiveness of my quads. My hamstrings are VERY weak compared to my quads, and that can't be healthy.