I have been reflecting on the great bookstores I have visited. My favorite is Powell’s in Portland, Oregon. But there are many others. Book Culture, Nine Lives and the Strand in New York City. University Press Books, City Lights, Green Apple, and Moes in the Bay Area; the Seminary Co-Op Bookstore in Chicago (great for religion, but a wide selection beyond religion); the Harvard Bookstore in Cambridge, Massachusetts; the Elliot Bay Book Company in Seattle; Diesel in Los Angeles (like Nine Lives, small, but good selection); Politics and Prose and Kramerbooks in D.C. I would be interested in others.
Here are links to interviews with the owners of Book Culture and Diesel.