Hi Ben,
If possible, a doctor or therapist should have a good look at your knees, and suggest a course of action. Of course, they may just say "Tough luck, there's nothing we can do." If that's the case, I know people who have had some success with glucosamine and chondroitin sulfate supplements.
Medical studies are inconclusive about these (
http://www.wellsphere.com/endurance-...thritis/598411), but numerous people have mentioned that their knees aren't as sore when they regularly take the supplements.
The other thing you might look into are exercises to strengthen your thigh muscles - sometimes knee pain is aggravated by imbalances between the thigh and hamstring muscles.
Good luck, I hope you find a solution to minimize the pain so you can continue training.
Peter