My recipe for eliminating my knee pain:
Stretching
Losing weight
Cross training
Good shoes
I'm 46 and have had chronic knee pain when running forever. Bad enough that I would need to stop running for 6 months to 1 year at a time. When I added a comprehensive stretching program, I was able to avoid the sore knees for a longer period of time, but it still always came back. When I added cycling to the mix, it really eliminated it. Biking really builds up the knee's supportive and aligning muscles and tissues.
Now, I'm careful not to run on successive days and my knees are virtually pain free. I run M-W-F and bike on T-Th-Sat. Being able to exercise this much helped me lose the extra 50 lbs that were also stressing out the knees.
I believe that biking and running are very complementary types of exercise. I'm going to use cycling to train for an upcoming marathon. Since my knees wont hold up to the high running mileage required for training, I plan to use cycling for additional endurance conditioning.
Of course, every running injury is different, so what worked well for one of us, may not be the answer for all.