Hey Matt - noted the comment on my log. "Runner's Knee" can be a bit of a blanket term I'm afraid - there are a few things that can make the knee ache and will do in different places. But they're all effectively 'overuse' injuries that are caused by the biomechanics being slightly out.
First off identify where the pain is. Outside of the knee is likely to be ITB syndrome, and inside of the knee more likely to be Patellofemoral Pain Syndrome - Runner's Knee. The latter hurts more going downhill/down stairs etc, and is due to muscle imbalance in the quads. Stand the bad leg, foot flat on ground then dip the knee and watch where it goes relative to the foot. If it goes towards the second toe you're fine, otherwise it's likely to track inwards and that's not so good. You'll need to do this as an exercise, but force the knee to go towards the second toe - 20 or so reps two or more times a day.
If it's ITB syndrome then you have to loosen it up - there are a number of stretches that you can do - have a look at
http://www.nismat.org/ptcor/itb_stretch/index.html or on the web in general (if you google these things you generally get quite accurate infomration).
It might well be worth going to see a physio and mention what's wrong, but ask for a general biomechanical assessment to see what's causing it and whether there's anything else wrong in general - catch it before it catches you! and they'll be able to explain the exercises a bit better than I can in a comment! You will probably have to rest for a bit as well anyhow...