Tor.com polled readers for
Best SFF Novels of the Decade (warning, enormous comment thread) so I'll post my choices here as well as there. They included 2000 as well as 2001-2010, which I liked.
In alphabetical order, so as not to take all day judging and sorting. I probably overlooked some, and I didn't include many fine books I haven't read yet (I hear Daniel Abraham's Long Price Quartet is excellent, and Jo Walton's
Among Others isn't out until next Tuesday).
Altered Carbon - Richard K. Morgan (2002)
American Gods - Neil Gaiman (2001)
Bones of Faerie - Janni Lee Simner (2009)
Child of Fire - Harry J. Connolly (2009)
Declare - Tim Powers (2001)
Digger - Ursula Vernon (2005)
Farthing - Jo Walton (2006)
The Graveyard Book - Neil Gaiman (2008)
The Last Hot Time - John M. Ford (2000)
Little Brother - Cory Doctorow (2008)
Old Man's War - John Scalzi (2005)
Paladin of Souls - Lois McMaster Bujold (2003)
Rainbows End - Vernor Vinge (2006)
Revelation Space - Alastair Reynolds (2001)
Shelter - Susan Palwick (2007)
Soon I Will be Invincible - Austin Grossman (2007)
The Twelve Kingdoms: Sea of Shadow - Fuyumi Ono (2007)
It makes me sadder than I can say that I'll never be able to put a Mike Ford book on a "Best of the Last Decade" list again. I'm glad 2000 was counted as eligible for this one.