The San Francisco Public Library has come up with a great idea: The Family Pass, which is available through December 31. The pass can be checked out for a week at a time and is valid at a huge amount of local museums (but only valid at one museum visit per week).
Here's how it works: There's one pass per branch, per museum, and the pass availability can be found online. The passes are available on a first come first served basis and must be picked up in person upon their due date. It takes a little leg-work, but it's worth it!
Also, we just learned that SFMOMA has family days on first and third Sundays, which include family tours and special programs, and kids get in free!