Have you ever heard about Patellar tendinitis? According to Runner's World,
"Patellar tendinitis is inflammation of one of the knee-joint tendons. Tendinitis occurs when tissue breakdown outpaces regrowth, and is caused by increased mileage, hills (especially downhills), and pace. Running through tendinitis will make it worse and prolong your recovery, says Davis. But treated early, it can heal in a few weeks. Here's how: cross-train, ice, wear a patella strap, take anti-inflammatories, stretch, and do exercises to strengthen the joint and quadriceps, such as leg extensions."
As I was laying in bed, I was thinking that perhaps it would be a good idea to use some heat cream on my knees (we don't have ice in this house). Alas, I couldn't find it, but stretching and massaging a bit did help! :)