I haven't the experience to back it up, but I have become a firm believer in stretching both the back of the knee and the tendons/muscle that extend the knee. There is a tendon that goes in front of your hip joint that is connected to the knee extender. Stretch that one, too.

A little disclaimer - I haven't been doing that for long. Seems promising so far. I've had only minor knee problems - typically not really painful, just uncomfortable "something's not right"-kind of feeling after overdoing some running or whatever. I've also overstretched from time to time, but that's quite a while ago.