Raggle, are you running every day? If so, it might help to have a day off in between just to give your knee a rest. I do this when I've done a lot of climbing on the treadmill and end up with the achy knee. My right knee is definitely dodgy. Also, good shoes will help. I know when the knee starts aching regularly that it's time for new shoes.
Today I did the 5k course at work and added a little bit so that I'd get to 50 minutes of walking. It was a beautiful morning, so there was no way I was working out inside.