Santa Ramen in San Mateo is the best and most unique ramen I have had in the bay area. Get the pork (tonkatsu) flavored ramen.
Santa Ramen
1944 S El Camino Real
San Mateo, CA 94403
(650) 344-5918
Other honorable mentions actually in San Francisco are Iroha in Japantown, Oyaji on Clement and Katana-Ya downtown.