If I was to do a top 10 in no particular order other than being numbered:

1.  Shadows of Destiny PS2

2.  Uncharted 2 Among Thieves PS3

3.  Ratchet and Clank Tools of Destruction PS3

4.  Devil May Cry PS2

5.  Grand Theft Auto San Andreas XBOX

6.  The Elder Scrolls IV: Oblivion XBOX

7.  Orange Box PS3

8.  MASS EFFECT XBOX 360

9.  Bioshock XBOX 360

10. Borderlands PS3

Also keep in mind that this is my opinion and games can come and go from this list (Gears of War 2, God of War 1 and 2 can easily be there). There is so many great games from the 2000's and there were many I just didn't get around to playing (Shadow of the Colossus).