Renovated and re-opened as of May 1, 2010!
The self-proclaimed "only museum devoted to the art, history and natural sciences of California" is well worth the BART trip for anyone interested in the art, history and natural sciences of California :)
Close to the Lake Merritt BART station (and Lake Merritt itself), the museum is about 30 minutes from downtown San Francisco.
Address: 1000 Oak St, Oakland, CA
Website: http://www.museumca.org
Wikipedia: http://en.wikipedia.org/wiki/Oakland_Museum_of_California