I have read, and recommend, the following books as having helped me get my head around the gender debate and wtf is going on. Please add your own recommendations...
Galileo's middle finger by Alice Dreger on activism and witch hunts in medicine and academic
As Nature Made Him: The Boy Who Was Raised as a Girl by John Calopinto
An essential account Dr John Money, gender identity proponent and of David Reimer's experience of being "raised a girl" after a horrible accident during circumcision.
The Coddling of the American Mind: Coddling of the American Mind: How Good Intentions and Bad Ideas Are Setting Up a Generation for Failure by Jonathan Haidt and Greg Lukianoff
The Righteous Mind: Why Good People are Divided by Politics and Religion by Jonathan Haidt
iGen: Why Today's Super-Connected Kids Are Growing Up Less Rebellious, More Tolerant, Less Happyand Completely Unprepared for Adulthoodand What That Means for the Rest of Us by Jean Twenge
And just for fun, Ben Elton's Identity Crisis and JKR's Strike series