Ooohh we have quite the club going. I have Chondromalacia in both knees and have just finished PT. Make sure you ice your knee after riding. I recommend you buy Andy Pruitt's Complete Medical Guide for Cyclists. I know Im always raving over this book but it really is jammed full of great info. It has a section on Chondromalacia and a section of stretches to help the condition especially strengthening the Vastus Medialis.

Avoid pushing big gears and until you get the condition under control avoid lots of climbing.

Hope this helps and GET ANDY'S BOOK.