I agree with tallbird that leg strengthening exercises help - but they have to specific to running. Its no good using machines in the gym.
I recommend the following exercise, both on one leg:
(1) Knee bends - stand on one leg and bend your knee 20-30 degrees and then straighten. Try to do without holding on to anything. Start off with 2-3 sets of 10 reps. When you get good do 10 reps, then without resting, do 10 reps of 10 seconds each, then again with resting reel off another 10 reps. This will leave your legs aching. When you can do this, start adding weight, dumb bells first, then bar bells, adding 5-10lb with each progression.
(2) One leg squats. With a chair at knee height, "sit down" with one leg and just touch the chair, but don't sink down. Then stand-up on that same leg. Follow Frank Horwill's Muscle Fatigue Saturation method. Do as many reps as you can, then rest for 1 minute, then again do as many as you can on the same leg, rest for a minute, then do one more set, again as many as you can. Rest for 2 minutes before doing the same for the other leg.
These exercises are tough but worth it - your legs will become really strong! And you will run faster and should help overcome knee problems.
If you try it out, let me know how you get on.