Ah, the Randall Museum... that glorious savior of parents with bored kids on a rainy day!
If you've got some sprogs in the Bay Area and aren't familiar with this valuable institution, you owe it to yourself to learn more.  The Randall Museum is a free museum, located on a hill overlooking the Upper Haight and the Castro disctricts that offers eductaional programs and exhibits, a small collection of local wildlife (my kid loves the visible bee hive!), and various programs and events.  It's a great alternative to the crowds and the expsense of hauling ourselves out to the Academy of Science or the Exploratorium (not that those aren't excellent resources).
Perhaps my kid's favorite part is the Golden Gate Model Railroad Club's basement model train room.  Multiple tracks are set up in the basement running beautiful trains through tiny cities and mountains.  They operate on Saturdays only, but it's a worthwhile way to while away an afternoon.