Have you had a bike fit? Your saddle may be too low.
Here's one of the better summaries on the web about cycling and knee pain, including chondromalicia (I've had mild chrondro. for many years):
http://www.cptips.com/knee.htm
I keep my saddle fairly high, and also switched down to 165 mm. crank length.
"My predominant feeling is one of gratitude. I have loved and been loved;I have been given much and I have given something in return...Above all, I have been a sentient being, a thinking animal, on this beautiful planet, and that in itself has been an enormous privilege and an adventure." O. Sacks