People are super surprised that there are very few cake/cooking stores here. You'd think there would be a bunch!
Peninsula has Sugar and Spice in Daly City. Big store, they have quite a selection for everything from cakes to cookies (BIG cookie cutter section) to candy making, but their mark-up is, ahem, insane. I always check Global Sugar or Amazon before I go there.
In the East Bay you have Spun Sugar in Berkeley. Nice cute little store, decent selection mostly focused on cake. They also have a nice chocolate selection. But again, they are a little pricey but they do have a parking lot, which is nice when you are going to a store on University Ave.
Other that that, I know of no other more professional grade stores that carry stuff other then Michaels.