Golden Gate Park is the best place to start a run. You can find everything from mild hills (through the park), to track runs (Kezar Stadium) and continue to the coast and along the Coastal Trail, which is beautiful. Besides Richmond and Sunset, you could start in Cole Valley or the Haight (and they get slightly more sun than Richmond/Sunset.

The Sunset and Richmond Districts both border Golden Gate Park which is ideal for running.

Living in SOMA gives you direct access to the Embarcadero. It's a flat run with a Bay view from the Ball Park, up toward fisherman's wharf. If you are an ambitious runner, you could keep going across the northern tip of SF, through the marina green and across the Golden Gate bridge!

If you want flat, you're best off in the Marina, which is completely flat (Chrissy Field, etc) or near Golden Gate Park, which is rolling (Richmond or Sunset). If you can hack the hills, try the Presidio, or Lyon Steps. Pac Heights and Cow Hollow offer good access...

The reason I chose to live in Marina is because there are no hills, which means it rocks for running. But if you really like hills, there are tons near by. The breeze from the bay helps keep you cool as well, which is another reason why the marina and running makes lots of sense.