If you plan to visit Alcatraz as a destination, make sure you understand the logistics of buying tickets for the approved ferry. Alcatraz is part of the National Parks and is free to visit...but there's only one ferry service contracted to actually bring you to the island to disembark. Tickets can be purchased in advance and any given service time may sell out. Other companies will advertise service, but they can only circle the island and bring you back to the mainland. (At least this is how it all worked when I visited a handful of years ago.)

If you're a baseball fan, you can check if tours of Giants stadium are available during your visit. Also, the Disney Family Museum is located inside the Presidio. It was created by the Disney family, not the corporation, so there's lots of interesting insights and family mementos.

San Jose is a bit outside SF, but I rented a car for a day trip, since I've always wanted to see the Winchester Mansion. The tour was quite extensive, both inside the house and outside around the grounds. During my visit, photography was not allowed inside the mansion due to a contract for an upcoming film. The movie's since been released, so I'm not sure how that stands now. Photography was allowed outside the building.