This is a good collection of top 5 or so places to run in San Francisco. Although, as they say, the best running route is the one that you'll actually end up running on regularly - which usually happens to be a loop starting from your home/work.
If you have any favorite routes, please post them below for everyone!
This is one of the most well written and authoritative guides on running I've ever seen. I got introduced to the run-walk method through this, and it has helped me go from barely being able to complete a 5k to finishing a half marathon.