Try
Southwest Airlines. A cheap, no frills airline (no food, used to be no assigned seats--not sure now, very quick and usually on-time flights, very popular, very simple ticketing rules, have to book directly on their website--don't think they are listed on any of the larger travel sites).
And look for Oakland or San Jose CA as other destination airports--Southwest does not fly to SFO. Not great transit in California compared to Europe and other places--but it is there
BART /
CalTrain as a start for Bay Area travel to/from the airports. Bart is for East Bay/Oakland Airport, San Francisco/SFO Airport. CalTrans is Bart connection (near SFO), south of San Francisco to San Jose (and near San Jose Airport).
Some times I look at the airport websites to see which airlines serve them, then check their websites (not all airlines are on the shared booking systems).
Otherwise, a couple of large websites to check flights on:
Orbits and
Travelocity. Have used both and they work fine.
Another option for cross US flights (or from Las Vegas to Los Angeles) is
Jet Blue. Very good prices and pretty good in-cabin service too.
-Bill
PS: There are the normal airport shuttle services and taxis. Many times it is cheaper to book a limousine than take a taxi at the stand (SFO Taxis are very expensive compared to most other options).
And you can look for
Grey Hound Bus Lines for other inexpensive transportation options (even from LV to SFO if you have a long day to ride the bus)