1999 - Soul Calibur
2000 - Diablo II
2001 - Halo
2002 - GTA: Vice City
2003 - Call of Duty 1
2004 - Half Life 2/WOW (hard to pick)
2005 - Resident Evil 4
2006 - Gears of War
2007 - Portal
2008 - Braid
2009 - uhhh...don't have a clue

My favorites of 2000-2009:

DC: Jet Grind Radio (2000)

GC: Ikaruga (2003), Viewtiful Joe (2003), Pikmin (2001), Fire Emblem (2005)

DS*: Sonic Rush (2005)

Wii*: Wii Sports (2006), Zack & Wiki (2007) , Mario Galaxy (2007)

WiiWare*: World of Goo (2008)

*Have yet to get to New Super Mario Brothers Wii, Punch Out, Wii Fit Plus, Wii Sports Resort, Your Shape, and Dawn of Discovery.

*Have a big backlog on DS - Layton 2, Civ Rev, World Ends with You...and stuff like Scribblenauts to get still.

*Have yet to play Nyxquest, intend to buy Lost Winds 2 and a few others by the end of the year.

1999:-
-SoulCalibur
Final Fantasy VIII

2000:-
-Shenmue
Resident Evil Code: Veronica

2001:-
-Final Fantasy X
Halo: Combat Evovled

2002:-
-Metroid Prime
WarCraft III

2003:-
-Star Wars: Knights of the Old Republic
SoulCalibur II

2004:-
-Half-Life 2
Grand Theft Auto: San Andreas

2005:-
-Resident Evil 4
Ninja Gaiden

2006:-
-The Elder Scrolls IV: Oblivion
Gears of War

2007:-
-The Orange Box
Resident Evil 4: Wii Edition

2008:-
-World of Goo
Super Smash Bros. Brawl

1- Civilization IV
2- Rome: Total War
3- Warcraft 3
4- God of War
5- God of War 2
6- Call of Duty 2
7- Fallout 3
8- World of Warcraft
9- Simcity 4
10- Europa Universalis III

The decade isn't over til Dec, 2010.

Still...

2001: Halo: it may not be a fantastic game, but being in college when this dropped offered hours of drunken killing in the dorms.

2002: Metroid Prime: Easy choice.

2003: Star Wars KOTOR: Easily the best Star Wars game and an altogether great western RPG.

2004: Half-Life 2: I'd still consider it the best overall FPS I've played.

2005: Psychonauts: It didn't perform well sales wise, but I thought it was the most original game of the year.

2006: I have to leave this one blank, nothing really stood out. I might have picked Twilight Princess, but I found it to be a disappointment.

2007: Bioshock: Literally dripping with atmosphere, except for some RPG's it pulled me into it's world much more than other games.

2008: Little Big Planet: It definitely had problems, but I'm a sucker for local Co-op and my friends and I have had a blast with this game.

2009: Uncharted 2: Surpasses the original in every way, closest I'll ever get to being in an action movie.

No Ico or Shadow of the Colossus on these lists depresses me greatly.
That said, I suck at years so I'll just list ten (in no particular order):

Ico
Shadow of the Colossus
Half-Life 2
Metal Gear Solid 3: Snake Eater
Deus Ex
Beyond Good and Evil
Super Mario Galaxy
Baldur's Gate 2
Uncharted 2: Among Thieves
Call of Duty 4: Modern Warfare

Eh, probably forgetting something. Oh well.

1999 - Command & Conquer: Tiberian Sun
2000 - The Legend Of Zelda: Majora's Mask
2001 - Super Smash Bros. Melee
2002 - Metroid Prime
2003 - The Legend Of Zelda: The Wind Waker
2004 - Star Wars: Knights Of The Old Republic 2: The Sith Lords
2005 - Resident Evil 4
2006 - The Legend Of Zelda: Twilight Princess
2007 - Super Mario Galaxy
2008 - Super Smash Bros. Brawl
2009 - Dead Space: Extraction

2000 - Majora's Mask
2001 - ICO
2002 - Metroid Prime (maybe Eternal Darkness, this was a good year for the Gamecube)
2003 - Star Wars: Knights of the Old Republic
2004 - Half-Life 2
2005 - Shadow of the Colossus
2006 - Wii Sports
2007 - Super Mario Galaxy
2008 - Wii Fit
2009 - New Super Mario Bros Wii (wahoo)

This list is subject to change whenever the Hell I feel like it.

Some of you are totally not objective rofl

That's because choosing a list of the best games of the decade, which is based on opinion, is supposed to be completely subjective.  You can not have an objective "Top ten games of the decade", it's a complete impossibility.