Joseph-Beth is a true rarity these days: an independent bookstore the size of a B&N, with great service and a wonderfully local focus on Pittsburgh writers. They have the best literary magazine selection in the area (that I've found so far) and a door to the neighboring Caribou Coffee.
My favorite sections here: the magazines, the poetry, the cookbooks, and the local books. They also have a wide selection of graphic novels, and offer a membership program for frequent shoppers (though I have yet to try this out).