When you going again? Read that the new Terminator film will be shooting in SF & New Orleans for a 4 & a half month shoot, with shooting commencing end of April.
1: Golden Gate Bridge
2:Fisherman's Wharf pier 39 sea lions and check out the USS Pampanito, a WWII submarine museum and memorial, and Ghirardelli Square.
3:Golden gate park .
and of course a visit to china town for rare Asian steelbooks
You guys could drive about an hour (depending on traffic) to the north and do this.
Head south to Monterey and see the aquarium, Pebble Beach and 17 Mile Drive. Check this link for more info. 17 Mile Drive is great and so is the aquarium.
There are also a few different State parks where you can see the Redwoods, etc.
Rent a car for a day and do the wineries in Napa or Sonoma, there is a Walt Disney Museum, Sausalito (went to the Trident restaurant there), and Lombardi street
aside from the normal stuff mentioned (Alcatraz, Fisherman's, Trolley, etc...)
Rent a car, and drive the coast-we renting a Ford Mustang some years ago, put the top down, and did a self-guided tour of a few 'movie-themed' stops...lots of fun, and included the original house from 'The Birds'. Went to 'Bodega Bay' and the restaurant where a few scenes were shot. A few years before that we also rented a car with a bunch of friends and drove to Napa, not into wine, but it's gorgeous out there. Definitely ride the trolleys (just part of the San Fran experience), and there a few cool museums there as well. This is the site I used as a loose guide when we went a few years ago http://www.citysearch.com/best/sanfrancisco but there are many others, as well as a few good 'off the beaten path' type guides for a quick overview.
Try to walk on the Golden Gate...often windy up there, but the views are very cool. If you go to the top of most of the streets and look down (it's quite steep to walk up there), but the bay view is pretty as well.
my wife and i missed out on the trams and the winding road, but we did get to ride a cable car and ride back to the wharf via the the iconic steep roads via cab so that was a real result!!!!!!!
I do not know about the whole San Francisco but I have been to Monterey and Carmel. So, I can suggest you about them both. Carmel and Monterey both are the places where you have lot of things to do and enjoy. Below is the list of fun things to do in Carmel/Monterey :
In Monterey :
Monterey Bay Aquarium - Sprawling marine life attraction