I would make the comparison to "Upstate New York" [0]. I like this Wikipedia article more than the one for Northern California because it admits that "there is no clear or official boundary between Upstate New York and Downstate New York".
The same is true for Northern and Southern California. There's no official distinction. Calling the Bay Area part of Northern California places too much emphasis on the Los Angeles area. By analogy, saying that "North" begins at the Transverse Ranges is like saying that "Upstate" begins at Yonkers. Ridiculous.
The Bay Area is not Northern California. It is Central California. Examples of places in Northern California include Yreka, Eureka, Redding, and Klamath Falls.
I have found that (Bay Area subset of N. CA) is a very common misconception of people who have recently moved to the area.
http://en.wikipedia.org/wiki/Holocene_extinction