I lived in San Francisco for several years and it's where I met my husband - miss it terribly. A bit of advice: if you are going to be there for more than a few days, go the DART/Muni websites (probably can easily find them from the City of San Francisco website) and check out their commuter passes. They use to have weekend or week-long passes (in addition to the regular month or yearly passes) that can save you a bunch if you plan on riding the cable cars, buses or underground subway. You can always purchase a pass at the kiosk that's close to a major stop (i.e. the Powell Street line where it ends between 4th & 5th Streets on Market Street - my office use to be @ 4th & Market). Be sure you pick up a map!
Don't hesitate to try one of the neighborhood restaurants - they're usually the BEST places to eat - use to be a Japanese noodle shop off of Judah that was to die for and cheap! Ha's is off the Judah line and is great chinese food - yummy green bean dish... For fun in the sun - go to Baker Beach - just be warned - the closer you walk to Golden Gate Bridge, the scantier the clothing! And for the best martini with the best view - head down the coast to Half Moon Bay and go to Moss Beach Distillery - it has a ton of history and the "Blue Lady" ghost! Favorite place of mine to eat and relax away from the City. And if you go a bit further down the coastal highway, a great beach to go to is Pescadero State Beach - has a wonderful rocky bar you can walk out on to see great tide pool creatures and also dig for mussels - however, not during an "r" month.
For the warmest, friendliest church you'll ever meet - St. Francis Lutheran - located at the corner of Church St. & Market. Sometimes we'd get unusual characters off the street - but that made it more real! It survived both the 06 and 89 earthquakes and is a beautiful red-brick gothic style church.
Have fun - it is a magical city!
Gail