Originally Posted by badger_biker
Try doing some quad and hanstring stretches before you ride. I experienced what sounds like similar pain earlier in the year and was concerned heading into a weeklong trip. I did the stretches each day and it helped significantly. Obviously this won't resolve a fit problem that may be causing it, but it shouldn't hurt and may ease your riding discomfort.
+1. It sounds like you're describing patellofemoral syndrome, which is a less severe deal than chondromalacia. It does have to do with the way the kneecap tracks over the femur, and it can usually be corrected with quad strengthening exercises, particularly in the last 15 degrees of the range of motion, i.e. try some leg bends where you only bend the leg about 15 degrees.
I'm no orthopedic surgeon, but that's what it sounds like. Definitely see a doc if it doesn't get better soon. No point messing around with your knees.