
John Crowley's masterfulLittle, Bigis the epic story of Smoky Barnable, an anonymous young man who travels by foot from the City to a place called Edgewood—not found on any map—to marry Daily Alice Drinkwater, as was prophesied. It is the story of four generations of a singular family, living in a house that is many houses on the magical border of an otherworld. It is a story of fantastic love and heartrending loss; of impossible things and unshakable destinies; and of the great Tale that envelops us all. It is a wonder.
John Crowley was a rare breed among American writers in that he was an accomplished science fiction and fantasy writer who was also recognized by the mainstream establishment. Harold Bloom included Little, Big in his "The Western Canon", for example.
I've not read the later Crowley works, but The Deep, Engine Summer, and Little, Big are all among my favorite books.
Hilary Mantel is very good. I haven't read the Wolf Hall books, but A Place of Greater Safety is beautiful and deserves to be better known.
I would also nominate Gene Wolfe, especially The Book of the Sun. Fits very well with the subject matter of Nabokov, as it is also a clever metatextual puzzle, albeit a very different kind.
Most popular books become obscure books, given enough time. (Reading Les Miserables, I had to consult the footnotes repeatedly for Victor Hugo's allusions to then-popular novels and novelists, almost none of which remain popular today.) If you're a serious reader the chances are diminished that your favorite book is something that has just recently been written. But it's also likelier than random chance that your favorite book was once popular, because as you note there's generally a positive correlation between quality and popularity.
