Pursuing such a subject is utter madness, of course, which is why I decided to crowdsource things last night. And boy, did people deliver! But being an unenlightened despot, I want to list my own choices - ini no particular order, some conventional, some more off the beaten track, and easily subject to change - first, before turning the proverbial floor to everybody else:
MYSTIC RIVER, Dennis Lehane (2001): Looking back I can still remember what a game-changer this book was, not just in terms of elevating Lehane's own writing and style, but in blowing up even further what a crime novel can, and should, accomplish with regards to character and emotion.
CASE HISTORIES, Kate Atkinson (2004): another of those books that widens one's horizons of what a crime novel should accomplish, and almost a near-perfect brew of witty phrases, pithy humor and deep melancholy. The other Jackson Brodie novels are very good, but this is the best.
BURY ME DEEP, Megan Abbott (2009): yes, it is early, but yes, it is that good.
FARTHING, by Jo Walton (2006): The whole trilogy (HA'PENNY and HALF A CROWN) all measure up, but this established Walton's utter mastery of alternate history (what if the Nazis and the Brits had brokered "peace in our time"?) and traditional mystery. I'm still kind of in awe of these books, actually.
TOKYO YEAR ZERO, David Peace (2007): The rhythm, the sentences, the utter and total despair and the absolute beauty of Peace's stark vision. The Red Riding Quartet is great, but this (and the follow-up, OCCUPIED CITY) totally knocked me out.
THE BLUE TANGO, Eoin McNamee (2001): The way he interweaved the real-life murder of an Irish woman in the 1950s with a dream-like, claustrophobic style impressed the hell out of me - and set up his very unique blend of "faction" that recurs in later books like 12:23 and THE ULTRAS.
STILL LIFE, Louise Penny (2006): It's not the best of the series, but it established Penny as the Queen of New Traditionalism, i.e. rethinking Agatha Christie for the 21st Century.
THE MILLENIUM TRILOGY, Stieg Larsson (2004-present): I'm lumping all three books together because in a way, they have to be taken as a whole in order to parse what a global phenomenon the books are.
JAR CITY, Arnaldur Indridason (2003): Mankell started the Nordic Crime boom, but Indridason, I believe, put the most indelible stamp on this subgenre.
THE SMALL BOAT OF GREAT SORROWS, by Dan Fesperman (2003): his work of late has been more overtly espionage and politically minded but this is still my favorite, and the one I feel best merges larger political themes (of the Balkan Wars of the 1990s) with more micro concerns of individual murder.
THE ICE HARVEST, by Scott Phillips (2000): this is how you do noir.
THE LINCOLN LAWYER, Michael Connelly (2005): truth be told, it's a toss-up between this and CITY OF BONES (2003), but the edge goes to Mickey Haller and Connelly's ability to inhabit the legal thriller mold in his own detail-oriented, express-train way.
THE BUSINESS OF DYING, Simon Kernick (2002): For the pure, unadulterated glee I felt while carried along with the voice of Dennis Milne, that no-good cop who was so bad and so great at the same time.
EVERY SECRET THING, Laura Lippman (2003): Her books have only gotten better since, but this was the one that showed where she was heading, and what story risks she was willing to take that didn't fit in the Tess Monaghan universe.
ABSENT FRIENDS, SJ Rozan (2003): For tackling 9/11 head on with grace and with care.
THE NIGHT GARDENER, George Pelecanos (2006): It's not my all-time favorite Pelecanos - that would be THE SWEET FOREVER or the DC Quartet as a whole - but it's the turning point of his newer, more controlled, mature style that we're going to see persist for a while.
THE POWER OF THE DOG, Don Winslow (2005): Sure, THE DAWN PATROL is kickass-tastic and almost everything he's written is great, but this is Winslow's great, underrated epic, a panorama about the drug trade that says more than you thought you'd want to know that turns out to be everything you must know.
WINTER'S BONE, Daniel Woodrell (2006): For the beauty of the writing and how much Woodrell packed in, emotionally and narratively, in just under 200 pages.
Truth be told, there's probably a good list of 50 books that could easily qualify for "best of the decade", and maybe by the end of this year a good consensus list can be built. What surprised me, though, were how many books I wanted to include that were published in the late 1990s which I view as something of a turning point for crime fiction as it is being published now. Enough of me, though, what say everybody else?