The Children's Creativity Museum, formerly known as Zeum, just reopened in mid-October.
The museum focuses on kids ages 3-12, and on creativity, collaboration and communication. It's a great place and one I recommend to any families visiting San Francisco.
If you're a Bank of America cardholder, you can visit visit the museum for free on November 5-6, through the Museums on Us program (which we use!). The card allows in one person, so if you and your spouse/partner each have a card, you each get in free.
A bunch of other San Francisco and Bay Area museums participate, so check out which ones.