Knees...

patellar tendonitis:

pain in the: causes:

front of knee seat too low (raise seat)
(anterior) seat too forward (move seat back) climbing too much (reduce climbing) big gears, low r.p.m. (spin more)

                    cranks too long (shorten cranks)
                    poor bike fit.

inside of knee
(medial) cleats- toes point out (modify seat position--->toe in. consider floating pedals.)

                    floating pedals (limit float to 5 degrees)
                    exiting clipless pedals (lower tension)
                                      feet too far apart (modify cleat position- closer.  shorten bottom bracket axle.  use cranks with less offset).   

outside of knee cleats- toes point out (modify cleat-->toe out. consider floating pedals. )
(lateral) floating pedals (limit float to 5 degrees)

                    feet too close (modify cleat position-->apart.  longer bottom bracket axle.  use cranks with more offset.  shim pedal on crank 2 mm.)

back of knee saddle too high (lower saddle)
(posterior) saddle too far back (move saddle forward)

                    floating pedals (limit float to 5 degrees)

*significant warmth/redness may indicate infection and requires prompt medical attention)

• in most cases, rest, ice, compression, elevation of the ailing bits are helpful.
  
  
  

chrondomalacia: a grating sensation at the front of the knee, pain going down stairs, and a general ache, stiffness after prolonged seating are frequent features.
caused by excessive force pushing the kneecap onto the surface of the femur (thighbone) causing excessive stress (called loading or shearing force) on the underside of the kneecap
and may result in it's surface becoming roughened. roughening of the kneecap can also be caused will posture imbalance, or anything that causes the kneecap to stray from it's ideal path.
a relative weakness of the inside or medial quadriceps muscles is often responsible. a wide pelvis or knock knees may make the condition more likely.

bicycling done correctly often helps this problem.
make sure knee is not bent more than 25 degrees from horizontal when your foot is at the bottom of your stroke
move seat back/ sit farther back in the saddle.
spin more. maintain a cadence of 85 rpm or more. avoid hills, especially long climbs. stand more when climbing avoid long cranks.
if pain is due to a tracking problem, rather than a load problem, pedals allowing some free rotation may help.
avoid squatting, kneeling, exercises that bend the knee more than 90 degrees. going walking/running down stairs/hills, or doing anything that increases load/shearing force of the patella on the femur.
strengthening medial quadriceps may help.