I prefer independent bookstores because the people behind the counter there love books as much as I do, and I can tell that by their eagerness to help me and to talk about books with me.  In general, I feel less of a personal connection with staff at chain stores, if any at all.  Independent booksellers also tend to be characters, with interesting personalities, and are a great source of tips for new books to read.   I once read a psychological thriller, House of Leaves by Mark Danielewski, because a staff member at Elliott Bay Book Company recommended it, even though I had given up reading that type of book years ago, and I'm so glad I did.  It was incredible, just fantastic.

  Also independent bookstores tend to display and bring to your attention different books than chain stores do, and in my experience they stock a wider variety of books, whereas chain stores stock more copies of bestsellers and mass market books.

  In general, their architectural spaces tend to be more creative, quirky, homey, and interesting.  They have less fluorescent lighting and more nooks and crannies, more open doors and windows for fresh air, more brick or hardwood floors, etc.  I enjoy the uniqueness of their physical environments, as opposed to the sameness of that in chain stores.

  Those are the thoughts that come to mind about why I've always preferred independent bookstores.  In addition to these reasons, I read this article on Elliott Bay Book Co.'s website a couple years ago about how chain stores affect the bookselling market and it strongly reinforced this preference.  It's written by the owner and I think every booklover should read it:  http://www.elliottbaybook.com/about/chains.jsp