San Francisco offers so much to see and do! I highly recommend a visit to the California Academy of Science in Golden Gate Park... this place has an aquarium, planetarium, and rainforest all inside. The shopping in Union Square is great; Fisherman's Wharf is touristy, but offers spectacular views; the Cliff House and beach is nice; Chinatown has some great finds for cheap prices; and don't forget to catch a Giants game at AT&T park.
For the cost-conscious (like myself!) the Cable Car Museum is nice for a quick visit (and free!); walking across the Golden Gate Bridge makes for a fun afternoon; stay away from costly cabs... buses are the way to go around here (ask for details at your hotel, try "511.org," or just do an internet search for "San Francisco muni.")
Even with everything we did, we still have more we want to see and do in the future!