What exactly are you looking for? I've been able to find a pretty good selection at the Berkeley Bowl in Berkeley. Many are sold in bulk. The only thing specifically that I have not been able to find (in the East Bay at least) is mesquite flour. I've heard that they might sell it at Rainbow Grocery in SF, but I haven't had time to look.
I think it would help if you were more specific. Are you new to the area? Can you give examples of flours that aren't readily available at supermarkets?
If you are new to the area, then you might not know about Whole Foods Market's bulk food section. Whole Food's bulk food section is significantly larger (and cheaper) than the bulk food sections at Mollie Stones and Andronicos. It is not as large, but almost as cheap, as the bulk sections at Berkeley Bowl (East Bay) and Rainbow Grocery (San Francisco). However, Whole Foods does have North Bay locations in San Rafael and Mill Valley (coming soon to Novato). http://www.wholefoodsmarket.com/store...
Unfortunately, the flour selection is a little different at different Whole Foods locations. The Mill Valley location's bulk section looks smaller than the San Rafael location's, but the Mill Valley location has more of what I like to buy. The San Francisco California Street location has an even better bulk section.
I don't know what you're looking for, but the North Bay locations should have a selection of organic and conventional pastry flour, whole wheat flours, bread flour (high protein), rye flour, corn flour, soy flour, rice flour, spelt flour, gluten flour, amaranth, buckwheat flour, gluten flour, garbanzo, etc. Again, note that some locations have a better selection than others.