Flying into San Francisco (SFO) and Oakland (OAK) airports both afford easy transportation into the city using the BART train headed towards downtown. From there you can take buses, taxis, cable cars or even ferrys to get to your destination, or else arrange pickups with your host.

Local public transportation can be found at http://511.org/
(see Transit -> Trip Planner)

Southwest has great fares (mostly into Oakland), and they are not listed on the bulk travel sites (such as kayak, orbitz, etc..)

Usually checking Southwest and one of the bulk sites like kayak will find you the best fares.

Check flights on Southwest Airlines: (for airports San Francisco and Oakland)

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