To the casual book buyer, Borders and Barnes & Noble might appear to be the same mega-bookstore with different covers. They're not.
Borders, for example, stubbornly persists in shelving memoirs among fiction. You'd expect -- I would expect -- that memoirs would be shelved along with biographies and autobiographies. Borders doesn't have such a section. Instead, biographies are randomly distributed throughout the store. A biography of Henry Ford, for example, would probably be found in the section on American history. This is an annoying practice.
On a positive note, Borders tends to leave books on its shelves longer than Barnes & Noble, and to offer a greater variety of titles. Each October I go in search of the five books shortlisted for the National Book Award. This year I had purchased two of the books -- Marilynne Robinson's Home and Peter Matthiessen's Shadow Country-- well before the shortlist was announced. I found the other three books at Borders.
If Barnes & Noble ever had these books--The End by Salvatore Scibona, The Lazarus Project by Aleksandar Hemon and Telex From Cuba by Rachel Kushner--they could not have been in the store long. Barnes & Noble seems to have a company policy of pulling books and returning them to the publisher after only a few weeks on the shelves.
Borders also appears to stock a greater variety of science fiction and mystery titles.
Independent bookstores are far superior to either chain in stocking a greater variety of books and in keeping those books longer. My inclination is turn to the independents first. But when I have to choose between one of the mega-stores, I know Borders is more likely to have the title longer than Barnes & Noble.