My hunch is that in the Bay Area, most apartments are in fact on Craigslist. The exception that I'm aware of are apartments rented by primarily non-English speakers, such as places in SF Chinatown and other highly ethnic neighborhoods. There you might find listings in a local Chinese-language newspaper or on a bulletin board at a small store.
I've never lived in the Bay, so I can't say. But I've recently done apartment searches in San Diego and Phoenix, and by far the strategy of most landlords is just to put up a "For Rent" sign with a phone number outside.
