Chondromalacia (AKA-"Runners Knee"

I looked at your blog, and you self-diagnosed as patellofemoral pain syndrome (PFPS). Not sure if that is the same as chondromalacia. In any case, I had PFPS back in summer/fall of '05 in one knee, and then again in winter/spring '06 in the other knee. I did do a stint of format PT for it.

In a nutshell (off of my memory), PFPS is usually instigated by tight hamstrings and/or weak quads causing your kneecap to track poorly. As a result of running, you get pain in the upper knee/lower quad. Or at least I did. Almost all of my PT exercises were designed to stretch and strengthen both the hamstring and the quad. I remember doing a ton of hamstring stretches, leg lifts, theraband exercises, and other low-impact activities. Avoid squats, lunges, and weights until the pain goes away, but then after that there will probably be a place for the heavier stuff. Oh, and I stopped running for several months. That helped too. I did find that the hamstring stretches especially helped.

You can also try deep massage. That has worked some for me. Get a tennis ball and go nuts on your lower quad. Or get a real massage.

In any case, seeing a physical therapist at least once for some testing will help you isolate what your exact problem(s) are, and then the therapist will set up a program for you to follow. Being a runner, you are probably very self-motivated, so you can do most exercises at home and in a gym, so I would avoid going to multiple PT sessions simply to save time and money (I've wasted plenty of both).

Best of luck.