Alcatraz is worth the visit, and the 'after dark' tour is especially good: it's extra moody and you get to go into parts of the prison that are normally off limits.
Rent some bikes down at fisherman's wharf and bike along the waterfront and over the GG bridge to Sausalito. Spend an afternoon there, then take the ferry back.
For food, you can't really go wrong, but some of my favorites are the Magnolia Brewpub on Haight and breakfast at the Boudin bakery on the wharf.
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