About your knees, you can try low impact plyometric exercises. A high impact choice like depth jumps may only aggreivate the problem.
After your normal leg workout try something like jump squats with just the bar, or squating down w/o the bar and from that position see how many times you can jump while breaking parallel the entire set.. Burpees also, and tabata squats of which there are vids over at crossfit.com.
The idea behind this is that explosive movement forces your muscle to expand and contract in a different way than anaerobic exercise. This provides a safe way to strengthen the ligaments and connective tissue around your joints that are used during your leg workout.