Biking is a great way to work your legs without taking a toll on your knees. To work the separate muscle groups in your legs it pays to pedal with clips, or straps, that secure your foot to the pedal.
Emphasize the downstroke: If you push on the downstroke you will work your quads - the muscle in the front of the thigh. This is also considered the most efficient stroke.
Emphasize the upstroke: Pulling on the upstroke will work your hamstrings - the muscle in the back of the thigh. While this technique is not the most effective for endurance riding, it will help you with sprints.
Emphasize smooth: Peddling in circle - this method will work your calves nicely. You hear this style called out a lot by Spin instructors. You imagine drawing a smooth circle with your foot as you're pedaling. This keeps the weight of your foot consistent through the entire stroke.
Experiment with different pedaling techniques and take full advantage of your leg power. Try this on the stationary bike at the gym, or if you have pedal clips on your own bike try them out on the road.