For several years now Bookworks has been my favorite small bookstore in the city. I like the intelligent selections and the deceptively large stock for such a small space. The latter is probably because they run the place as a store and not a museum of print, and don't fill the shelves with some of the junk other bookstores allow to pile up. And the kicker here is the steady flow of review copies and other "new" books available at remainder-like prices. That plus the store is well-lit, clean and has aisles wide enough to accomodate multiple browsers ... not your typical dusty-attic style used bookstore.
Pros: Intelligent catalog, Wide selection, Excellent prices
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