The jolly giant of Berkeley independent bookstores. City Lights Books. Don't miss the poetry room. Harvard Book Store. Dealing in used books, both scholarly and general, they've got an excellent selection and rapid turnover in most subjects, and they're now in a fabulous neighborhood.
Prices are generally quite low.
Starr Book Shop. In the back end and basement of the Harvard Lampoon building, this shop stands out for its tremendous selection of review copies of recently published books, which are now conveniently sorted by publisher. Also has a decent selection of other used books, especially given the relatively small size of the shop, and the prices are reasonable. Lame Duck Books. An antiquarian shop specializing in modern European philosophy and literature.