Amazingly I've been to two of the nominees: Leon's and Dudley's! On the basis of one black and white, Leon rules.
Dudley's: Big on reputation, short on follow-through. I live in the area and have been there off and on for 30 years, and they sell their bread in many supermarkets in San Diego. It just isn't special, IMHO. In fact, it's usually doughy and undercooked, but the tour bus crowd loves it. I think it's rep was built when there was nothing to see, eat or do between San Diego and Julian and Sunday drivers needed a diversion, a goal, a bit of baked goods. You get so darn hungry even Mom's super-sweet apple pies taste fantastic. But I am in the minority, everybody seems to love both Dudley's and Mom's.
So I will nominate the West Gin bakery in San Marcos (CA) and raise you Bread et Cie in Hillcrest. West Gin (VietNamese) for French pastries, and Bread et Cie for, well, bread. Well I will nominate any VietNamese bakery, because there's another great one in Mission Viejo near the auto mall. And I will defintely check out AA Bakery on Stockton SF, thanks for the heads up, number_6