The two big off-campus new book bookstores are Kepler's (in Menlo Park on El Camino) and Printer's Inc. (on California Ave in Palo Alto). Both give 10% student discounts if you show your student ID card up front.
Both have adjacent cafés, which are a fine place to hang out (providing you don't mind the odd Powerbook-user at adjacent tables).
There are numerous other bookstores around. A pair of good used bookstores near the bookstores mentioned above are Wessex books (around the corner from Kepler's) and No Knew Books (on California Ave, and which also gives a student discount). Check out Chimaera (University Ave., Palo Alto) and Bell's Books (Emerson St., Palo Alto).
Berkeley is specially blessed with a large number of bookstores. Moe's on Telegraph Avenue has a fine collection of used books, many of which are actually of interest to linguists.