None of my short story nominees made the Hugo shortlist. (I think that my very favorite was Corrine Duyvis's Eight, or possibly Seanan McGuire's The Tolling of Pavlov's Bells.)
I'm less certain about my ranking for the short stories than I was for novels; I feel less strongly about these ones. I wasn't really enamored with Mike Resnick's The Homecoming; E. Lily Yu's The Cartographer Wasps and the Anarchist Bees was beautiful but I think I failed to Get the last line (and thus, probably, the point); Ken Liu's Paper Menagerie was a good story, but it revolves around a broken mother/son relationship. I'm still in the early years of motherhood, when you're terrified you're going to lose your kids to a peanut butter sandwich down the wrong pipe; I am not cool with having the concept put into my head that one could just walk away from me, all on his own. NOT COOL.
So that leaves:
#2: The Shadow War of the Night Dragons: Book One: The Dead City: Prologue, by John Scalzi
This was an April Fool's joke story: a fake excerpt from a book whose title is a mashup of the most common words in fantasy titles. I've read grumbles on the internet - or perhaps grumbles about grumbles, I can't remember anymore - that an April Fool's joke doesn't belong on an award ballot. Which seems silly for a genre that treasures The Hitchhiker's Guide to the Galaxy and pretty much anything written by Terry Pratchett. I liked this story a lot; it cracked me up. I'm a little sad it isn't a real book.
#1: Movement, by Nancy Fulda
This story is about an autistic girl who has the chance to become "normal". It's told in first person, through her eyes, so the voice is very different. It was thoughtful and hopeful and sad, all at once. If you had the chance to get rid of your greatest weakness - or what the world sees as weakness, anyway - but it would simultaneously change everything that you are, would you do it?