San Francisco is an awesome town (perhaps the best place to visit in the US). It is unique, has great food, and there is always something going on. One of the best parts about SF is the day trips you can do from there. I suggest giving yourself the full 5 days - exploring all the great suggestions above - and then doing a day trip to one of the following:
Here is a page on Napa Valley with kids:
http://gocalifornia.about.com/cs/nap...canapakids.htm
To the south is Monterrey:
http://www.mbayaq.org/
Muir Woods National Monument (where you can explore the giant Redwoods) is pretty close to the north
http://www.nps.gov/muwo/