Joseph Fox Bookshop, is the best bookstore in the city. It's a small, independent shop that's been in business for over 50 years. The staff are knowledgeable and willing to help you find whatever you need. JFB doesn't have the breadth of titles that you'll find at one of the big chains, but every book here is worth reading. There's no junk on these shelves, and no tsotchkes - just quality books. They have a great selection of new fiction and non-fiction, and there's a small (but well-chosen) children's section in the back.
It's located on Sansom St, just a few blocks north of Rittenhouse Square.