The Metreon and the San Francisco Center Century Theaters are closest with the mall theater just edging out the Metreon as being closer. 845 Market St. - top of the mall.
If you want to treat yourself - pay a little more and go the extra mile (via cab if you have to) - and go to the Kabuki Theater in Japantown. It's part of the Sundance Cinemas and you can reserve your seat online (tickets are on sale now for Harry Potter). That way you don't have to spend time waiting in line to rush in and grab good seats.
There is a bar and bistro food available at the theater as well.
It's always my first choice for movies in San Francisco. I think because the price is a bit higher you have fewer people talking during the film, or talking back to the screen.