I learned a new stretch in yoga this week that was MADE for runners and their dodgy knees!
First get a blanket or towel, and a yoga block or something of similar dimentions (my yoga blocks have all been kidnapped by the little people, and I’m using a box of flour here. worked fine). Sit as if you were going to move into ustrasana (camel pose): knees hip-width apart, tops of feet firmly pressed into the ground, box/block/whatever inbetween your feet.
Sit back onto the block, adjusting height as needed, and hold for several breaths. That’s it! It stretches the backs of your knees as well as the front, and gently works out any aches and pains around your kneecap.