Jason Sanford has posted up his nominations for the Nebula, Hugo, and Locus Awards. I already agree with some of it, and hopefully will be able to track down other that I haven't read. Unfortunately, there are a few stories that I probably won't be able to because they're published in print zines that don't let their fiction out for free (unless it has already been nominated and then only during the voting period).
Also, I'm not sure about the eligibility of Paolo Bacigalupi's The Alchemist. Or, Tobias Buckell's The Executioness, for that matter (not on Sanford's ballot, but it's a linked story). Sort of like Mary Robinette Kowal's "Water to Wine", they were first published in 2010 by Audible.com and then in print by Subterranean Press in 2011. Like MRK's novella, absolutely worth nominating if you feel strongly about it. Worst case, it gets enough votes and we get a ruling on cases like this.