Below, you'll find some good stretches and exercises for working the hips and glutes, which many experts now attribute lots of injuries, including knee problems. Runner's World also has a video of some of these and others available here. If you have ANY questions on these, PLEASE let me know - rather make sure we are doing them correctly, rather than wasting your time or worse, getting further injured, by doing them incorrectly! - Coach Phillips

Eagles - make sure shoulders stay on the floor.  
Calf Drops (see calf raises below) - just drop your heel off the step to get a good stretch.  
Single leg stand in bare feet for 30 seconds (just start w/ a slight knee bend, and gradually add more time).  
Single leg stand in bare feet for 30 seconds w/ eyes closed (just start w/ a slight knee bend, and gradually add more time).  
Bridges w/ kick - a little tougher. Make sure you squeeze your glutes and abs... and try not to engage the hamstring so much.
Bridges w/ hip lift Lie faceup with your legs sharply bent. Place your left foot flat on the floor and draw the right leg up against your torso, holding it in place with pressure from your hands. Now contract the hamstrings and buttocks of the left leg to lift your butt off the floor two or three inches. Concentrate hard on keeping your deep abs contracted and your pelvis neutral. Hold this position for five seconds and relax. Repeat five times and then switch legs.

Fitzgerald, Matt (2007-09-04). Brain Training For Runners: A Revolutionary New Training System to Improve Endurance, Speed, Health, and Results (Kindle Locations 1970-1973). Penguin Group. Kindle Edition
Calf Raises - do 3 x 15: toes pointed in, toes pointed straight, toes pointed out. You can do the calf drop for a count of 15 between each of these for good rest.  
Fire hydrants - 2 x 15 each side
Clamshells - 2 x 15 on each leg
Leg lifts - 2 x 15 on each leg
Single leg hot foot - for 30 seconds, do a cross on the floor: jump slightly forward then right then back then left then forward, right, back, left... then switch legs  
Squats, wall squats