I wish that more of my original nominations had made it to the final list, but that's the way it is. That being said, you really should read Warren Ellis's graphic story Aetheric Mechanics.
Without further ado...
("About time too!")
I heard that.
(1) Truth by Robert Reed (Asimov’s Oct/Nov 2008)
(2) The Tear by Ian McDonald (anthology Galactic Empires)
(1) Pride and Prometheus by John Kessel (F&SF Jan 2008)
(2) Shoggoths in Bloom by Elizabeth Bear (Asimov’s Mar 2008)
(3) The Gambler by Paolo Bacigalupi ( Fast Forward 2)
(4) Alastair Baffle’s Emporium of Wonders by Mike Resnick ( i>Asimov’s Jan 2008)
Best Short Story
(1) Exhalation by Ted Chiang (Eclipse Two)
(2) From Babel’s Fall’n Glory We Fled by Michael Swanwick (Asimov’s Feb 2008)
(3) Evil Robot Monkey by Mary Robinette Kowal (The Solaris Book of New Science Fiction - Volume Two)
(4) Article of Faith by Mike Resnick (Baen’s Universe Oct 2008)
(5) 26 Monkeys, Also the Abyss by Kij Johnson (Asimov’s Jul 2008)