Where to start?!
The great thing about the bay is you can live close to the city without having to pay a city mortgage.
The best affordable neighborhoods really depend on what you're looking for (single family home, condo, number of bedrooms etc) and what your budget is. Are you renting or buying? Which side of the peninsula you prefer and so on?
Some suggestions right off the bat would be Daly City or South San Francisco if you're looking to be on this side.
Feel free to call me if you have any more questions and I'd be happy to help.
Better Homes and Gardens Burlingame