My running has been plagued by bad patella tracking and therefore knee pain. Poor patella tracking is typically due to weak Vastus Medialis Oblique (VMO) muscles and tight quads. I have tried doing many different VMO exercises but they came up short. I did many leg extensions and leg presses and even though the VMO was worked in these movements I never found it adequate in developing VMO strength. Doing some squats as a test of strength for my physiotherapist revealed a lot. He could see flexibility problems and strength imbalances with my knee buckling as I descended into the squat position.
So what is the answer? The answer is squats. Squats work the quads, buttocks, and VMOs like nothing else (plus they teach the VMO to fire at the right time). To begin, first perform progressions such as step-up and split squat variations. The step-up squat is done by placing the foot of first leg on bench. Stand on bench by extending the hip and knee of the first leg and place the foot of second leg on bench. Step down with second leg by flexing the hip and knee of first leg. Return to original standing position by placing the foot of first leg to floor. Repeat first step with opposite leg alternating first steps between legs. For the split squat you squat down by flexing the knee and hip of front leg until the knee of rear leg is almost in contact with floor. Return to original standing position by extending the hip and knee of the forward leg. Repeat. Continue with opposite leg.
Once you have developed the proper strength from these progressions you may perform full squats. To do these you descend until knees and hips are fully bent. Extend knees and hips until legs are straight. Return and repeat. One of the many reasons full squats are extremely beneficial is their ability to develop the VMO and make them fire properly. Going to the full squat position places the VMO is a fully stretched position under a load. Other great exercises are the rear lunge, side lunge, single leg squat, and the walking lunge.
My physiotherapist has often spoken of his ability to cure knee problems of athletes just by utilizing full squats and their variations. For me, squats were the only thing that has made a difference to my knees. It was painful at first, but I stuck with it and now am reaping the rewards.