The best place in Berkeley is Looking Glass (Telegraph at Oregon - nearest BART would be Ashby), though their equipment inventory isn't high. Consumable supplies are decent, and they still provide darkroom rental. They have a small web site at http://www.lookingglassphoto.com/ The staff is generally young but practising photographers. They are open Sundays, which doesn't apply to the big SF stores. For a small operation their prices are competitive. Certainly cheaper than travelling to the city or Palo Alto if you are on the east side of the bay. If you are looking for something specific, call first these days.
The Santa Clara photo fair is a mix of private dealers and store-front names. Camera West and Midwest had tables at the last one, for example. It was a crush. The next one is Jan 21st - http://www.photofair.com/ The Hayward events are smaller - http://camerabooks.com/custom.aspx?id=23 .
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