Thinking about the short fiction in 2008, one of the writers whose work really stands out is Elizabeth Bear. In 2005, she won the John W. Campbell Award for Best New Writer. And in 2008, her story "Tideline" won a Hugo. Her novel forthcoming in 2009 will be the Norse fantasy By the Mountain Bound.
She published several really superb stories in 2008.
• "Shuggoths in Bloom," which just made this year's Hugo ballot, was published in Asimov’s. It is an extraordinary contemporary Lovecraftian story set in about 1939 off the coast of Maine, and constitutes an original reinterpretation of some elements of the Chthulhu mythos. The atmosphere of cosmic dread is particularly well established, and the New England setting spot on. (It will appear in our Year's Best Fantasy 9, forthcoming from Tor.com.)
• Her collaboration with Sarah Monette, "Boojum" was published in the excellent original anthology of fantasy and SF pirate stories, Fast Ships, Black Sails, edited by Jeff and Ann VanderMeer. It turns the premise of the anthology on its head. A tale of living spaceships and brain-thieves, this story, in the tradition of Anne McCaffrey's The Ship Sang, is one of this year's most entertaining. That one will appear in our Year's Best SF 14, forthcoming from HarperCollins.
Her stories were among 2008's high points for me.