I remember family car trips as a series of factory tours. Some were more interesting than others. The canned tuna tour was nightmare-inducing. The Hershey's tour was much better. In the East Bay there used to be just one chocolate facility you could tour, but now there are two factories within spitting distance of each other- Scharffenberger and Charles Chocolates.
Scharffenberger is really all about the transformation of the beans to the bar. To see how it happens, you make a reservation and then you sit through a presentation on how chocolate is made and finally see the factory itself. After the tour, you can head to the cafe or retail shop. There is also a virtual tour.
At Charles Chocolate, the factory is also attached to the retail shop and there are long glass windows that allow you a great view of the action. While not exactly a tour you can see chocolate confections being made by a team of candy makers. Any time the store is open, you can take a peek.
My suggestion? Make a reservation at Scharffenberger, take a break for lunch and then head over to Charles Chocolate. Both offer a fascinating glimpse behind the scenes. You won't have Willy Wonka as a guide, but the experience will be scrumpdiddleumptious nonetheless.