Unfortunately, knee pain is not that uncommon among serious runners and cyclists. If the pain is one that comes and goes, seems to be located on or under the knee cap, and is aggravated by squatting, bending, kneeling, or going down stairs, more than likely you have what is referred to as chondromalacia.
orthoseek.com offers some exercises to help improve the condition. Pronation, hill running, tight, fatigued or weak quadriceps, running on the same side of the road, and overuse are common causes.
cptips.com offers tips for cyclists here. Incorrect seat position, cranking too much against high resistance, and incorrect cleat alignment are all possible causes.