Monterey Bay Aquarium is amazing
http://www.montereybayaquarium.org/
Santa Cruz Beach and Boardwalk is tons of fun
http://www.beachboardwalk.com/
San Francisco has many of the touristy restaurants, Rainforest Cafe, Johnny Rockets etc on Pier 39. The Pier is a really unique place. There are street performers, shops, restaurants and the sea lions that have taken over the boat slips.
http://www.pier39.com/index.cfm
A Bay cruise under the Golden Gate, a trip to Alcatraz or a day spent riding the cable cars. My kids love, love, love riding the cable cars.
The California Academy of Sciences recently re-opened after a 500 million dollar renovation. I have heard really good things, it is located in Golden Gate Park.
http://www.calacademy.org/
The Exploratorium in San Francisco is a really fun place (we are headed there this weekend at the request of DD 11)
http://www.exploratorium.edu/
Couple of amusement parks:
Discovery Kingdom which was formerly Marine World, it has Animal shows and rides.
http://www.sixflags.com/discoveryKingdom/index.aspx
Great America amusement park as well as water park
http://www.pgathrills.com/#actions
There is a great water park in San Jose - Raging Waters
http://www.ragingwaters.com/
San Jose has an wonderful Childrens Museum, considered one of the best in the country:
http://www.cdm.org/index.asp?f=1
San Francisco has so many different dining options. There are wonderful cafe's, award winning restaurants etc. We are partial to a hole in the wall chinese restaurant in China Town and always eat there, so I can't help much with other restaurants. Yumm, we are eating there on Saturday!
Happy planning!