Okay, so I've finally figured out what my nominations should be, with less than a week remaining.
1: #114 Wolves Till the World Goes Down by Greg van Eekhout
2: #131 Skatouioannis by Nick Mamatas
3: #86 Tio Gilberto and the Twenty-Seven Ghosts by Ben Francisco
Runners up:
#88 Another End of the Empire
#92 Sir Hereward and Mr. Fitz Go to War Again
#93 Mermaid's Tea Party
Justifications
Wolves Till the World Goes Down is great for the themes of predestination, free will, and whether or not the gods are really puppets to destiny, or if they can effect their own change. Hugin's decision at the end is what absolutely makes this one for me. Funny, thoughtful, moving, and oddly hopeful for a story about the end-of-days.
Skatouioannis for inventing a monster that is both an angry, smelly old man with a donkey cart and shovel, and a metaphor for how the old ways can conflict with technology and science and try to keep anything from changing. Also for nanotech intersecting with poop-demonology. But mainly it's the metaphor thing I swear.
Tio Gilberto has very good writing, and a very awkward relationship where the semi-abusiveness of the older guy is genuinely creepy. The sadness of the story never becomes maudlin and there is a touch of humor thrown in from our comedian protagonist. "Sometimes I forget that for most people, realism can't be magical," is one of my favorite lines. The ending is left open in a superposition between horribly tragic and bitterly relieved. Also, Uncle Tio himself is one of the best tragic characters of the year.