I already did this for at the end of 2009 and I wouldn't include any of the new movies I've seen in 2010 ("Greenberg", "Toy Story 3", "Inception", "Scott Pilgrim vs. the World", "The Social Network", "Iron Man 2", and "Easy A") as some of the greatest of the last 10 years, but "The Social Network" is a close call and I might feel differently after seeing it again. At the moment, for the best of 2000-2010, I can't think of any past 2008:
1 "X2: X-Men United" (2003)
2 "Kill Bill, Vol. 2" (2004)
3 "Before Sunset" (2004)
4 "Traffic" (2000)
5 "Adaptation" (2002)
6 "Cidade de Deus (City of God)" (2002)
7 "Lost In Translation" (2003)
8 "High Fidelity" (2000)
9 "Forgetting Sarah Marshall" (2008)
10 "Sideways" (2004)
Those are just my personal favourites, but I think "Catch Me If You Can", "Requiem for a Dream", "The Wrestler", and "Donnie Darko" are just as great as any on that list.
To the person who started this thread: I really hated that Star Wars movie and I found "Clerks 2" really disappointing as I didn't think there was enough good material there for a whole movie, but "The Hangover" is a solid choice. Definitely one of the best comedies I've seen in the last ten years. Also, "The Boondock Saints" came out in 1999. Fun movie, but a little outside the range of your thread's years.