The Exploratorium--museum of science, art and human perception in SF. We may have to save this one for next year.
Palo Alto Junior Museum and Zoo--very small and inexpensive (free, with $3 suggested donation), with a nice playground and the local Children's library right in the same area! Nice for a mellow day close to home (or Grandma's house, in our case).
Oakland Zoo--we really enjoyed this!! Lots of great animals with plenty of space, a fun kids' play area "Children's Zoo", and an adjacent rides area with carnival like rides--my favorite was the train ride overlooking the zoo and going through an area with wallaroos and emus, the kids also liked the carousel and airplane rides
Children's Discovery Museum in San Jose--we loved the WaterWays area and the Wonder Cabinet the most!!
awesome play space in Berkeley, CA with art studio, dance studio, puzzles, play kitchen, dollhouse, nursing room, run room (with balls, roller coasters, climbing, tumbling), blocks, stage, puppet theater, dress up, magnets, library reading room, light room, eating room, crawlers room, outdoor playground, and outdoor water area (outdoor stuff is seasonal)
Adventure Playground in Berkeley, CA--awesome space with materials and tools for kids to create and build. Also has an awesome zip line!!
Adventure Playground - City of Berkeley, CA
Model Train and Trolley display at the Conservatory of Flowers! Nisa and Shaiah will love this!
List of fun places to visit in the Bay Area
Bay Area Discovery Museum - The Bay Area Discovery Museum is a one-of-a-kind indoor and outdoor children's museum at the foot of the Golden Gate Bridge, serving over 300,000 visitors per year on its 7.5 acre Sausalito campus. The Museum is the only children’s museum in the U.S. to be located in a national park, and its exhibits are admired and emulated by other children’s museums nationwide.
Malibu Redwood City Amusement park