The Girl Who Chased the Moon is one of my favorite books by Sarah Addison Allen. And actually, it was the first book that involved me enough to allow me to see past the device when I first got an e-reader. While I wasn't a huge fan of the original hardcover I looooove the whimsy of the paperback.
I have yet to read Diane Setterfield's Bellman and Black, but I loved the original hardcover, and I think the new paperback edition might be even more ominous.
Ready Player One, by Ernest Cline, is a huge fan favorite. While some people clean, retro flavor of the hardcover, I adore the detail in the paperback edition.
After Dark, by Haruki Murakami, is one of those books I'd like to revisit. While I think the colors in both editions are spectacular, I'm particularly partial to the paperback. In person, each little dot sparkles silver against the sleeping face and dark backdrop. It's ethereal and fits the mood of the book so well.