I think qetta's right about patellofemoral syndrome (also known as runner's knee since lots of runners, including me, get it). Here's another link from a running site: http://www.coolrunning.com/engine/2/....shtml#runknee
If you're doing any kind of exercise that puts a lot of stress on your knees (running, aerobics, martial arts, etc.) you should probably stop for a while. Biking is good while your recovering, and elliptical trainers are supposed to be fairly low-impact also.
I had a bad case a year ago. The first thing I did was to take ibuprofen for a week to reduce swelling and pain. You might also try icing your kneecap for 15 minutes or so twice a day. You may not see any swelling, but if you're experiencing pain, there's probably swelling behind your kneecap.
The next thing was to start doing exercises to strengthen the inner quads. Strengthening these muscles helps to keep your knee tracking properly as you bend it. Here's another good site with exercises: http://www.med.umich.edu/1libr/guides/knee/runknee.htm
I find that the wall squats work really well. If you're doing them right, you'll definitely feel it in your inner quads.
If you do some stretching and exercise and it doesn't start to get better within a few weeks, see a doctor (preferably an orthopedist or a sports medicine specialist). The pain you're feeling is caused by damage to the cartilage on the underside of your kneecap, and it's notoriously slow to heal if you seriously wear it away. Runner's knee can also lead to arthritis if untreated. Good luck! Many runners get runner's knee at some point, and it's totally treatable, so I'm sure you'll make a smooth recovery.