There are an amazing amount of Museums here in San Francisco.  Here is a list of most of them.

Asian Art Museum - Arts of India, China, western Asia, South-East Asia, Korea & Japan.  Located in the Civic Center area of San Francisco.  http://www.asianart.org/

Boudin Bakery Museum & Bakery Tour - See the history of Boudin and San Francisco with a catwalk view of the bakery located at Fisherman's Wharf.  http://www.boudinbakery.com/

Cable Car Museum - Located in the Nob Hill neighborhood at 1201 Mason Street, it has all the historical and explanatory exhibits of the San Francisco cable car system.  http://www.cablecarmuseum.org/

California Academy of Sciences - One of the ten largest museums of natural history in the World. It was newly remodeled in 2008 and is located in Golden Gate Park.  http://www.calacademy.org/

California Palace of the Legion of Honor - The Museum contains a representative collection of mainly European art, the largest portion of which is French.  The building is located in Lincoln Park in the northwest of the City.  http://www.famsf.org/legion/index.asp

M.H. de young Memorial Museum - The de Young exhibits American decorative pieces, textiles and paintings.  Its located in Golden Gate Park.  http://www.famsf.org/deyoung/

The Exploratorium - A 'hands on' museum of science, art, human perception and technology.  Locatd in the historic Palace of Fine Arts.  http://www.exploratorium.edu/

SF Museum of Modern Art - Showcases some of the best modern art in the country. Its located at 151 Third Street.  http://www.sfmoma.org/