There are a ton in the SF Bay Area. Here are a few:
CinemaWest is a small, local chain:
Fairfax 5
9 Broadway, Fairfax, CA 94930
Clover 4
121 E. First Street, Cloverdale, CA
Angels 5
1228 S. Main Street, Angels Camp, CA
Fortuna 6
1241 Main Street, Fortuna, CA
Livermore Cinemas
2490 First Street, Livermore, CA
Contra Costa Stadium Cinemas
555 Center Avenue, Martinez, CA
Boulevard Cinemas
200 C St., Petaluma, CA
Sebastopol 9
6868 McKinley St., Sebastopol, CA
Sonoma 9
200 Siesta Way, Sonoma, CA
Tiburon Playhouse
40 Main St., Tiburon, CA
Noyo
57 East Commercial Street, Willits, CA
Christopher B Smith Rafael Film Center
1118 4th St, San Rafael, CA 94901-3007