Replying to Knee pain after running. halp?

i used to do track and cross country, and every day after a long run my knees would start to hurt. Sometimes so much that i had trouble walking down/up stairs. it was a bad aching pain in the joint. even now sometimes they get sore, or some tendon directly on the left or right side hurts. Im worried about hurting them this summer at hood. anyone know of any good strengthening exorcises, or know what is wrong with my knees