Many knee problems are due to a tightening of the soft tissues structures around the knee joint. If due to running or other excess exercise the ITB (iliotibial band) or the TFL (tensor fasciae latae) tightens, then this pulls the patella (knee cap) laterally (outwards). This creates pain and is the knees' way to let you know, you have created imbalance in your body.

If the Vastus Medialis (muscle on the inside and slightly above the knee) is weak, this in turn can create more pain. This muscle can be strengthened to balance the musculature. Contracting the quadriceps over the last 20 degrees of movement, hence straightening the leg will create strength in this muscle, not something like bike riding, where the leg is never fully straightened.

Most knee problems are created due also to the tightening of the hamstrings, this pulls the tibia (lower leg bone) towards the femur (upper leg bone) increasing the chance of impinging on the delicate nerves inside the knee joint. Just strengthening the vastus medialis and/or quadriceps muscles will not correct this problem long term.

Lengthening the hamstrings will help enormously by providing space within the knee joint. This is no easy matter, the hamstrings are very fibrous and resist stretching. Your patience and  a good yoga teacher are invaluable here. The positioning of the knee during some sporting activities, eg. knees turning inwards during surfing, places extra stress on the knee joints and so requires you to maintain healthy knees and long hamstrings to ensure your competitive longevity and problem-free knees.

Those sports that tend to stress knees include: football, soccer, gridiron, snow skiing, hockey and especially running and surfing. Many football, gridiron and hockey teams now employ yoga teachers on a regular basis to lengthen and balance players' musculature and as a result, reduce the incidence of knee injuries. I still see the most atrocious stretching techniques from "old School" coaches and players, who ignore advances in sporting performance research and practice "ballistic" stretches, leave out stretching altogether or consider that their sporting knowledge somehow 'confers' upon them knowledge of stretching/yoga, even though their bodies are as stiff as their players. Because I'm a yoga teacher does that mean I could go out and coach football teams how to play, I hope it doesn't.

If there is weakness in the arches, this can also lead to some knee problems. Arches can be strengthened as can any muscles. Tight hips can also place more strain upon knee joints as the hip is unable to absorb sufficient sporting shock or unable to absorb excess leg movement during impact conditions.

Surgery should be considered a last resort, once soft tissue has been taken out, this alters the whole biomechanics of the knee joint and you may find, as I have observed sometimes, that either your knee problems continue post-surgery or a new problem is created somewhere else. There are no quick fixes to long term problems.

There is also a need to look into the psychosomatic conditions that may contribute to some knee problems. Knees are seen as connected to excess ego and pride. If looking at these issues helps, then it is of benefit to the person concerned. It is also said that all injuries are caused from judgements from within, inner-juries. So it is probably worth looking inwards for the reasons and benefits of your inner-jury. 

Lessons in following intuition, knowing when to rest and/or wanting to pursue alternative careers (that you enjoy more) may also be the lessons involved.

Whatever the cause, it is your challenge and responsibility to deal with the things as they are and make the best of it. Finally, find a good yoga teacher (minimum 3 yrs training and biomedical knowledge) specifically trained in yoga-therapy, they usually understand knees from a theoretical stand and from practical experience, as their daily practice takes their own knees to a full ROM (range of movement) during their yoga practice.

They probably, like myself, have to deal with thousands of students each year, many of whom have knee problems. If you fully understand your own knees: bones, ligaments, tendons, muscles, nerves, energy flows and psychosomatic issues, then you are in a good position to help others.

You will need to consistently practice with awareness and patience. 
All obstacles can be overcome. Good luck.