Not in the Bay Area, but if you're ever passing through San Luis Obispo on 101, take the California St exit and head south 3 blocks to the corner of Calif and Monterey to FRANK'S.
Frank's Famous Hot Dogs serves a terrific b'fast burro with scrambled eggs, bacon, cheese, potatoes, salsa. WOW! it's pretty dang good. There are a couple of hot sauces at the condiment bar as well. About $3.50 or so, and huge. Frank's is our go-to b'fast stop when heading out of town early on a long roadtrip. Cheap, fast, and very clean spot. Burro served till 11:00 I think. After that you can get burgers, dogs, fries, shakes, etc.