There are many websites for running in the San Francisco area. East Bay Striders and Bay Area
Running Pages both list running routes in the Bay Area, and can also link you to other websites
with other routes.
Of course, running in the Bay Area usually means hills. If you have a car, my favorite run is
over in the East Bay, along Skyline Drive. You can park your car anywhere in Tilden Regional Park
and run either north or south to your heart's content. Your view is often overlooking the entire
Bay Area -- it's breath-takingly memorable. It's hilly, but not impossible. For a flatter run in
the East Bay, you may want to keep going over the hill to San Pablo Resevoir. I'm not sure of
the mileage, but it's a nice, flat bike route.
In SF, the running is more urban -- I like running up to Twin Peaks: it's quite a hill workout,
but getting to the top gives you the best view of San Francisco: downtown, Golden Gate, East Bay,
etc. well worth it.
Enjoy America's best city!