The first of these museums is the Cartoon Art Museum. You may wonder what your children can possibly learn from a museum such as this, but as with all art, comics often imitate life and this museum shows how comics have evolved and morphed over time. In addition to that, anything that will encourage your children to read is a good thing in my opinion, even if it is comics that they are reading.
Next, there is the Bay Area Discovery Museum. This museum offers hands on entertainment for children of all ages. While most exhibits are designed with children ages 1-10 in mind, there are plenty of activities and exhibits that will appeal to older children as well as those entertaining the notion of a second childhood. This museum offers many activities and adventures both indoors and out that will appeal to your children while teaching them about other creatures, cultures, technology, and the world at large around them. This is definitely worth having a look. Be sure to check and see if there are any events being offered while you are visiting.
If the Bay Area Discovery Museum isn't enough to get your little one's creative juices flowing and put you all into the supreme spirit of learning, then perhaps you should check out Zeum. Zeum is a multimedia arts and technology museum. By allowing visitors to hands on use of their equipment they are fostering imagination and igniting curiosity in the young minds of their guests. This is definitely unique enough for a closer look. I hope it spikes your inner techno guru as completely as it reached mine.
There are many more places than this that you can visit in San Francisco that offer an equal spark for the minds and imaginations of your little ones. But the fact remains that you know your child's interests and talents better than anyone else. Find those things that will appeal to each child's personality and that above anything else will make this trip special for him or her.
I also believe that it is important to allow your children an opinion on what to do and see while on vacation. You may be surprised to find the things that will appeal to them as well as the fact that they really do on occasion think about what you as a parent want for them. By giving choices and a voice you are teaching your children that they are important to you and that their opinion matters.