I'm a local, here are my favorites. I'd like to here some other suggestions. Mine range from somewhat posh to quaint.
Zazzie (you'll wait)
Out the Door (get the steak and eggs)
Brenda's soul food (introduce yourself to beignets)
Dumplings always good too.
1658 Market Street, San Francisco, CA 94102
Out the Door
1 Ferry Bldg Plaza, San Francisco, CA 94111