A couple things to maybe look into...

Has the surface you are running on changed at all?

Are you due for a new pair of shoes?

Have you recently been wearing new shoes? Are they the right shoe for you?

Have you been warming up enough before running?

Have you been stretching before and after?

Those are the first couple questions that came to mind. If you are still having achy knees on a consistent basis it might be beneficial to take some time off. I know that is everyones worst nightmare, but it is worth it. Maybe take a couple days off straight, but continue to do stretching then try running in the pool perhaps. The knees take a beating from running, but the pool takes the stress off the joints and is great for staying in shape without pounding on the pavement. If it persists I would see a doctor to make sure you aren't going to be doing more harm then good by running.

I hope you feel better soon.

Sara