I have PFS, but it's pretty much under control. I didn't get it from bike riding. (Don't try to study ballet and African dancing at the same time. S'all's I'm saying)
Streches are really important - particularly hamstring stretches, and quadricept stretches (pictued in link) and calf stretches.
http://farm4.static.flickr.com/3193/3037069558_c55f221fd2_o.gif
Be careful in the hamstreing stretch to keep you back straight.
For any of the stretches, make sure your legs are well-warmed up before you stretch and you hold each of the streches for about 30 seconds -which will seem like a very long time - and do them a minimum of twice each side.
The three second stretches you see guys do? They hurt and increase the risk of injury. Don't do them.
When I was at my worst, I did 4 streches, 30 seconds per side and six repeats. Lots of time on that.
For me, the quadricepts isomentrics helped alot, too.
These are specific things that worked for me - but I was not a bike rider then. The pattern of strengths, weakness, and imbalances between muscle groups that cause PFS might be way different for a biker.
I'm pretty sure that for 90%+ of dudes with knee or back pain, hamstring stretches are a key treatment, though.
Ice is therapeutic. In my experience. this is to the point where doing a little of the irritating exercise, then icing is dramatically better than rest.
Ibuprofen, should always be taken with food. That stuff (NSAID) kills about 16,000 people per year. Treat it with respect.
That said, NSAIDs not only treat the symptoms, they also help the condition. They can be taken "prophylacticly" - that is, take a small does before you begin the irritating exercise - to good effect.
Try to keep stretching as ahabit after the pain is gone. Joint pain gets worse with age.
If you have insurance, you want to get to a PT - they can give you stretches and exercises specific to your individual problem. PT's, in my experience, really, REALLY like helping people with their exercise programs and suggesting small details that make large differences.
As Mayhew and wsh point out, bicycle fitting and alignment is going to be critical, particularly with cleats. (shrug) That's a "D'uh" AFTER the pain starts.
Cross-training
In the past, I swam for exercise and just used a bike for transportation. This year, I trained for, and did, the Pgh -> DC -> Pgh trip, without doing other fitness stuff. My sense is that without cross-training, biking for fitness leaves one bizarrely imbalanced, vulnerable to injury, and not really all that fit for non-bike activiites. Maybe a small amount of cross-training can remedy this.
Disclaimer: I'm not a doctor, although I played doctor when I was a small child.
Good luck
Mick