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The quadriceps complex is a much more complicated structure than most people realize. Some muscles cross from origins on the hip, on the outer area, to attachment on inner sites below the knee, while others cross from the inside to the outside, and the most commonly noticed muscles make up the bulk of the over-all structure, in the front of the femur, passing the patella, and also attaching below the knee joint.
If the pain and discomfort is on the inside or outside of the knee joint, a possible cause is an imbalance in the relative strength and flexibility of the muscles that attach to that side of the joint. A Sports Physical Therapist, or a Certified Physical Trainer, with certification in rehabilitation exercise, may be able to provide exercises that will overcome the imbalance.
My knee joint pain, on the inside of my right knee, is lessened, by seated, leg extension exercise, with moderate weight, and consistent exercise. I also use a knee compression sleeve, covered by a soft knee brace - non-hinged. When an imbalance is corrected, overall quad, hamstring, and calf strength and flexibility are to be maintained. Running, by itself, in such cases, is not sufficient to avoid recurrence.
Some physiologists recommend the use of glucosamine, and chondroitin to aid in the maintenance and healing of joint and connective tissue.
Omega-3 fatty acids are also recommended, to ensure proper joint lubrication.
As mentioned by an earlier poster, ibuprofen can be used, before exercise, to avoid inflammation in the affected joint.
As with any lay-offered advice, consult with a trusted physician, before applying any such suggested remedies.
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To be good at a sport, one must be smart enough to play the game -- and dumb enough to think that it's important . . . 
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