mrissa's Tor.com story, "Uncle Flower's Homecoming Waltz", was awesome. I did read a lot of books, though, and these were my favorites that were eligible.In no particular order:
Lois McMaster Bujold, Captain Vorpatril's Alliance. Arguably a sequel/follow-up to Memory, this is Bujold in fine form.
Elizabeth Bear, Range of Ghosts. A really solid non-western epic fantasy, full of changing skies, steppe ponies, and hungry ghosts.
Robert Jackson Bennett, The Troupe. Manages to make American-inflected epic fantasy work, which is no small task. The teen protagonist made me wince with recognition.
Kameron Hurley, Rapture. God's War got all the attention last year, but Infidel (the second of three books) was better. Rapture, the trilogy's conclusion, is better still.
Mike Carey, Linda Carey, and Louise Carey, The Steel Seraglio. Not horror, despite being published by Chizine. 1001 Nights as filtered through a city of women - warriors, traders, diplomats, spies. I love this book to bits, and it deserves more attention than it's gotten.
Honorable Mention:
Ben Aaronovich, Whispers Under Ground. I love this series, and this book was just killer. That said, it didn't quite rise above the others on my shortlist.
Anyway, that's my novel ballot for this year.