The best source of new books in Classics is Borders, which you can access outside of SF. Perhaps UC Berkeley has a good selection of new Classics books - I haven’t had a chance to get a good look there yet since I generally don’t have a lot of spare time whenever I’m in Berkeley.
The SF State University Bookstore has a meager selection of Classics books. Last time I was there, about the only books they sold which were not availible at Borders were the Willcock editions of Homer, Cunliffe, and a really cheap edition of Crito in Greek.
For used classics books, the two most useful stores are Green Apple Books and Black Oak Books 2. Green Apple Books, on Clement and 6th Ave (directly availible by bus lines 44, 2, and near bus line 38), has plenty of Loebs, however most of their classics stuff focuses on Classics in Translation. Still, sometimes they have goodies, such as the copy of Aristophanes’ Clouds in Greek which has a full vocabulary in the back. Be sure to look in the Classics AND the Reference/Languages section, since some books on Ancient Greek tend to get shelved in the latter.
Black Oak Books 2, on Irving and 7th Ave (directly availible by N-Judah, near bus lines 71, 6, 66, 44, 43) has more advanced books on Classics, such as that in-depth commentary on Pindar’s Pythian Odes. It is the best source for non-Loeb books in Classical Greek. Since many of them are out of print, many of them are quite expensive. You can also check out the other Black Oak book stores - the original Black Oak bookstore is in Berkeley, and Black Oak Books 3 is in North Beach.
EDIT : Another place which sometimes has Classics goodies is Aarvark Books, on Church Street, near Market Street. It is availible by the J Church and F Market lines. Anyway, it’s the cheapest used books store in San Francisco, so it’s worth a look for almost anything. There are a lot of other used books stores in the area - while they tend not to have nothing in Classics, some of them have excellent selections of, say, books in French, or other topics.