Running

I gave up on the hopes for the latter years ago.

Deep squats. Seriously, it builds up the muscles that support and protect the knee. Can have the side effect of squatters bum, where you develop muscles in your arse that you didn't know you had. That and the quads you develop from mixing cycling and squatting can make finding trousers that fit a challenge.

Edit: oh, just to be clear, this is barbell squats, not silly bodyweight squats.

Good for the beginners:

http://www.sparkpeople.com/resource/exercise_demos.asp?exercise_type=lower