Eon, by Alison GoodmanRead about another entry on the list.
Eon has trained for years to be a Dragoneye—an apprentice to one of the twelve great dragons of good fortune. But he has a secret: He’s really Eona, a sixteen-year-old girl, and if she is discovered, it will mean certain and immediate death. This young adult novel is violent, complex, and dark, and it could just as easily be marketed to adult audiences.
The Page 69 Test: Eon: Dragoneye Reborn.
Also see: Ten of the best literary men dressed as women.