One title on Newitz's list of "stories that seem like fantasy at first, but the science fiction creeps up on you:"
The Steel Remains, by Richard K. MorganRead about the other stories on the list.
This hard-hitting fantasy tale of a man and his seriously badass sword-fighting abilities seems like your standard fantasy fare. It's full of castles and kings and different "races" of elves and humans and such. Until you start to realize that those elf-like guys are actually connected to something that isn't so much a magical place as it is a crashed spaceship. This novel is of the most satisfying genre-benders out there, and luckily for us the sequel (The Cold Commands) comes out this summer.
The Page 69 Test: The Steel Remains.
Also see: 10 works of science fiction that are really fantasy.