All good advise, but a couple of comments...

If you're talking about starting with your knee bent at a 90 degree
angle like this http://www.exrx.net/WeightExercises/Quadriceps/LVLegExtension.html
- these are controversial. I understand a lot PT's don't recommend
them anymore, even for healthy knees but particularly not for people
with PFPS (chondromalacia). One way to alleviate the risk is to only
work the upper range and stop with your leg halfway to the 90 degree
position. But the standard leg extension for PFPS is the straight-leg
raise. See http://www.santerehab.com/hurts/exercise/othr_kne.html

I'd be very careful with deep squats if you have chondromalacia. OK,
if they don't hurt (either while you're doing them or cause a "flare
up" within a day or two afterwards) and you do them in proper form.
(Of course this is ture for any exercise...) I submit that that many
with PFPS will have trouble doing them in proper form due to muscle
tightness, etc.

I had a very serious problem with chondromalacia several years ago.
I'm now generally pain-free, but I still get little flare-ups of it
now and then.

Here are the things I'd recommend, based on my experience.  (I should
note that I'm not a physician and that YMMV and all that stuff.)

* If you're not already doing it, start taking glucosamine/
chondroitin.

* Do leg extensions if they don't feel like they aggravate your
knees.  I find them therapeutic when my knees flare up.  I don't
bother with them unless I'm having knee pain.

* Do deep (below parallel -- a.s to grass) squats.  If you don't know
how now, learn this.  Start with no added weight if you're new to it.
Keep doing them after your knees recover, to help prevent future
problems.

* Do hamstring, quad, and achilles tendon stretches -- religiously,
twice a day.

* Avoid impact exercises like running or lots of walking,
particularly on pavement.  Avoid stairs when possible.  Avoid jumping
(well, at least the landing part :-) ).

 * Don't do the stationary bike if it hurts.  You might find an
elliptical trainer more comfortable.  Water exercise is also great for
someone whose knees hurt.  If a repetitive exercise is painful, it's
not a good choice for you.

 * Ice your knees if they're sore.

 * For always -- not just when your knees are bothering you -- avoid
twisting your leg with your foot planted on the ground.  

Good luck!

Chris

Crossposted to ASD and MFW for input.

Stats:
Female age 32yrs
5'3", 135lbs
workout with combo of weights and cardio

I've been dealing with knee pain for a while now and finally sucked it
up and went to the doc.   After a 45min wait in the waiting room,
another 15 in the exam room, a 10 min consult and doc says:

"Chondromalacia"

OK, so flash backs to highschool - this is what I had back then.
This is what is bothering me know.

Treatment:  PT, for 4 weeks.  Spend lots of time on the stationary
bike.  If no improvement, off to Othropedic for further treatment.

Now, the question is.....  What are the suggestions from those in the
group?   How do I handle workouts?

Running/jogging?  
Biking?
Weights?
Squats?
Lunges or deadlifts?

What should and shouldn't I do at this point.   I now have to go spend
time researching this to determine my next course of action.