xc29,
I too have struggled with knee issues. In my experience, I have dealt with knee pain two ways:
1) Often it signals I need a new pair of shoes.
2) Other times it signals I need to stop torquing the knee by running cross-country (which I prefer, and by your screen name I'm guessing you do, too). Moving to the track often eases the pain.
Once, several years ago, I was running cross-country and my knee hurt so badly I had to walk back to my car. On a hunch, I drove straight to the track. I was able to run at the track immediately, with no pain at all! I took some time off from running cross-country and my knee got better.
If you don't have a track, your local gym probably has treadmills.
I don't recommend paved roads if your knee is sore, for two reasons: roads are typically angled slightly which torques your knee, and pavement is always hard which jars your knee.
Dark Horse
I'm a dark horse, running on a dark race course.
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