There is New Pieces in Berkeley (lots of batiks and asians)[they are right off 880 (?). There is Always Quilting in San Mateo. There are a couple toward Fremont. There is Prairie Queen (off 17 near Camden) in San Jose and The Granary and Eddie's Quilting Bee in Sunnyvale, if you have a car.
Cotton Patch is over the "hill" from Oakland in Lafayette. It's a nice store, too.