It sounds like you have the same problem that plagues Rafa, patellar tendonitis also known as "jumper's knee" or as Chas has above "runner's knee".
Chas gave you some good references, although you find them somewhat technical.
WebMD also has some good information - and you may find it a little easier to digest:
Jumper's Knee http://www.webmd.com/fitness-exercise/jumpers_knee
Here's what it has to say on treatment:
Most patients respond to a conservative management program such as the one suggested below.
Activity modification: Decrease activities that increase kneecap and upper leg pressure (for example, jumping or squatting). Certain "loading exercises may be prescribed.
Cryotherapy: Apply ice for 20 to 30 minutes, 4 to 6 times per day, especially after activity.
Joint motion and kinematics assessment: Hip, knee, and ankle joint range of motion are evaluated.
Stretching: Stretch (1) flexors of the hip and knee (hamstrings, gastrocnemius, iliopsoas, rectus femoris, adductors), (2) extensors of the hip and knee (quadriceps, gluteals), (3) the iliotibial band (a large tendon on the outside of the hip and upper leg), and (4) the surrounding tissues and structures of the kneecap.
Strengthening: Specific exercises are often prescribed.
Other sport specific joint, muscle, and tendon therapies may be prescribed."
These are examples of exercises that may be of help once the pain has subsided:
Many have muscle imbalances, and can benefit from the E-exercises in Pete Egoscue's book Pain Free http://www.amazon.com/Pain-Free-Revo.../dp/0553379887
Posture Guy is an Egoscue therapist here on TT, and hopefully he will weigh in.
As wildvolley mentions above, once all the pain/inflammation has subsided, doing more heavy duty exercise by squatting could better strengthen the leg muscles than the above illustrated exercises that are meant more to start the rehab process.
Are you even one ounce overweight? If so, losing weight will decrease the stress your knees are under.
Some are fortunate enough to figure out how to treat themselves - but many do better getting help from a sports medicine specialist and/or therapist.
And be smart - give your knees a rest so they have a real chance to get better.