Most likely your knee problem is caused by worn or wrong shoes, running on non-level streets, running on indoor tracks, not stretching correctly or enough, going too fast or too far for your current body-condition. There may be other reasons, but these are the ones that come to mind right now. The stretches I do are here, but there are other good stretches. google on the three words running knee stretch or similar words.

As a suggestion, stop running until your pain subsides. Then cut your distance by half and run slowly. If the pain returns, see a good podiatrist about your shoes. If you still have pain, see a sports doctor for a checkup. To help get rid of the pain, use RICE.

Here is my page on knee injuries that will give you some introductory info plus other links.