If you're interested in Western history and rare books, Caravan Books downtown is a must. It's the last remnant of Bookseller's Row, and convenient to the main library, where you'll want to visit the children's reading room, which was formerly the main reading room where Bukowski discovered Fante.
Vroman's in Pasadena is a good 100+ year old general interest bookshop. Also Skylight in Los Feliz for zines and a good general collection with a hip focus. Hennessey + Ingalls in Santa Monica for art and architecture. Mitchell Books in Pasadena for mysteries. Wacko in Los Feliz for subculture and gift books. Oh, and Acres of Books in Long Beach hasn't been seized by the city yet--that's worth a couple of hours.