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As of right now, I can think of a few books that would fit in great with this class:

--Left Hand of Darkness by Ursula K LeGuin. It's a scifi novel about a planet in which all of its inhabitants are physically genderless, and then develop genitalia for a certain time of the month for mating. A human male travels to the planet to act as an ambassador, and it's his sense of gender versus theirs. There are other issues in the book as well, such as politics, religion, and knowledge vs ignorance,  but the gender is a HUGE part. I loved reading it, especially considering that the extreme majority of characters in the novel believe that having a "permanent gender," like the ambassador, is a disorder, almost something to pity.

--What Happened to Lani Garver by Carol Plum-Ucci.  Yeah, this is a Young Adult fiction novel, but it's pretty amazing. It takes place in a very small town, and the school receives a new transfer student, Lani Garver, who seems to defy every category people use to classify others - gender, sexuality, and age in particular. It's narrated by an "almost-popular girl" who befriends Lani, and is taught to completely change her outlook on life and realize that not everything is so easily labelled. The ending (which is revealed in the prologue, actually) is very heavy, though. 

-- Orlando by Virginia Woolf. I actually just finished reading this the other day, and it was fantastic. It's a fictional biography of Orlando, a boy who lives during Elizabethan times, and keeps on living to the present day (well, 1928). Orlando's gender also changes halfway through. Woolf is hilarious and talks a lot about how Orlando acts and thinks in each gender, and other societal commentary. She's... amazing.