Mast Books, East Village, NYC. Diverse selection of new/used books on art, design, philosophy etc. Gorgeous layout and excellent music choices too.
Palais de Tokyo Bookshop, 16eme, Paris. Huge selection of art books, many of which are discounted. The museum’s often got good exhibitions as well.
Foyles, Soho, London. The best of London’s big bookstores for browsing — very spacious, lots of seating, and tons of light.
The Strand, Union Square, NYC. Indoors is way too cramped and overwhelming, but if you patiently search the discounted sidewalk shelves you will always find a few gems (and get an interesting sense of people’s reading tastes).
McNally Jackson, Nolita, NYC. Big but not overwhelming, good lighting, expansive selection and curation that encourages serendipity. The Downtown Brooklyn location is good, too.
Popular places I don’t particularly like: Books Are Magic; London Review Bookshop; Shakespeare & Co. Paris (though the NYC one is okay).