sounds like runner's knee. glucosamine/chondroiton supplements are great, as mehm mentioned. i'd also just do a general google for "runner's knee" and check out some of the stretching/strengthening exercises they list.
best advice on treatment is not to do anything that causes pain for a week, but don't worry about anything that doesn't hurt it. the one tricky thing i've found is that it tends to improve dramatically w/in a couple days of rest, but you need to give it about twice that amount of time before you'll be ready to ease back into using it.