What are you looking for, more specifically? I second _Whipping Girl_ for an in-depth discussion of trans issues, but if you want trans fiction, you should check out Topside Press and Transgress Press (they publish authors like Casey Plett, Kelly Dunham, Imogen Binnie, and Sybil Lamb). Susan Jane Bigelow does sci-fi stories and novels with trans themes; Libba Bray's _Beauty Queens_ and Courtney Milan's latest contemporary romance have a trans character. Jenny Finney Boylan has a couple of trans memoirs out. Janet Mock has an autobiography.
Being Emily, Almost Perfect, Luna, and Just Girls are YA novels by cis authors that have trans main characters and handle it well.