There is often a strong link between knee pain and faulty biomechanics.  The first place you can address (with confidence that it will do no harm) is your Glute muscles.  Yes, even if you think you have buns of steel, you may not be using your hip Abductor and External Rotator muscles effectively, or they may actually be weak.  For most of us, we have to do specific strengthening of these very important Gluteal muscles because our activities of running and biking are in the sagittal plane which is not effective at strengthening these muscles.  The glutes are VERY important, as they control femur motion, specifically how it relates to the knee.  Weakness causes the femur to internally rotate, which causes poor patellafemoral tracking, IT band load, and ligament strain.  This weakness is easily combatted with both specific strengthening like clams and side leg raises, as well as very important functional strengthening like a single leg Curtsy lunges, 3 way kick with band, etc...

The second place to look, is your quads.  Quad tightness, specifically the VLO (due to its lateral pull), and the Rectis Femoris (also crosses the hip joint) cause increased loads of the patella on the femur.  Its all physics, so when the quads are tight, and when you bend your knee, the patellar load dramatically increases if there is tightness and trigger points in your quads.  Chronic compression of the patella against the femural groove can lead to chondral (cartilage) damage known as Patellofemoral pain syndrome (PFPS), AKA chondromalacia patella.

These trigger points and quad tightness can be helped by stretching.  However many times the "tightness" is actually muscles being in a contracted state.  These trigger points that have a better chance of releasingand elongating with foam rolling, trigger point release, and Wave Tool use. Use the Wave Tool on the quads, IT band, and around the knee to decrease muscle trigger points, adhesions, and stiffness in the patellar attachments.

Whats the answer for avoiding knee pain?  Keep your quads supple, keep the hip abductors strong, maintain patellar mobility, decrease unhealthy adhesions, and maintain proper strength relationships between different muscle groups.   

Check out the video section for  Knee Self treatment with the Wave Tool, as well as Lower extremity strengthening for athletes.

https://www.youtube.com/watch?time_continue=3&v=3aGhYnRKISc