How about visiting mazes or labyrinths? …about.com/od/…bayarealabyrinths.htm
I'd say most visitors to the bay area haven't visited museums/activities at Berkeley and Stanford. I'm more familiar with the Berkeley ones, but know Stanford has some, too (isn't there a sculpture garden or something). Berkeley Art Museum, anthropology museum, Berkeley Rep, Cal Performances. There are some computer/tech museums in San Jose and the Oakland Museum of California. Many small museums are in SoMa, which many people haven't visited.
Take some free San Francisco City Guides tours of neighborhoods in San Francisco you want to know more about.
There are many regional parks in the bay area for hiking, and even after being here for years I haven't been to them all. See bahiker.com for example.
It's too bad the blimp rides were discontinued, though they were quite expensive.
Tesla Motors is a bay area company that makes luxury electric cars--maybe they have tours or a showroom or something.
I assume you've been to Santa Cruz and Monterey. What about the mushroom festival in Morgan Hill or the Garlic Festival in Gilroy? (Depends when you visit.) There are often little festivals and other things at various times and places around the bay area.
Treasure Island hosts a flea market, I think it's the last Sat/Sun of each month (the view is the real treasure here). Angel Island is a fun place to hike, picnic, ride segways or visit the immigration museum.
I've thrown out a bunch of less common activities than the typical tourist things, anyway. Maybe some seem interesting to you.