I still haven't seen a large number of films from the most-recent decade (which began in 2000, not 2001) but I worry that if I wait too long, this list won't be relevant anymore. So here are what I currently think are the 'Top' films of the 2000's, in alphabetical order. The 'Top 10' are in bold.
(500) Days of Summer (2009) 2046 (2006) Artificial Intelligence: AI (2001) Avatar (2009) The Aviator (2004) Borat: Cultural Learnings of America for Make Benefit Glorious Nation of Kazakhstan (2006) The Bourne Identity (2002) Bowling for Columbine (2002) Burn After Reading (2008) Children of Men (2006) Choke (2008) City of God (2002) Crash (2004) Crouching Tiger, Hidden Dragon (2000) The Dark Knight (2008) Fahrenheit 9/11 (2004) The Fountain (2006) Grindhouse (2007) In the Mood for Love (2000) Inglourious Basterds (2009) Into the Wild (2007) Kill Bill: Vol. 1 (2003) Kill Bill: Vol. 2 (2004) Knocked Up (2007) Letters from Iwo Jima (2006) The Lives of Others (2006) The Lord of the Rings: The Fellowship of the Ring (2001) The Lord of the Rings: The Return of the King (2003) The Lord of the Rings: The Two Towers (2002) Match Point (2005) Moulin Rouge! (2001) No Country for Old Men (2007) The Passion of the Christ (2004) Requiem for a Dream (2000) Russian Ark (2002) Sideways (2004) Slumdog Millionaire (2008) Superbad (2007) Synecdoche, New York (2008) There Will Be Blood (2007) Traffic (2000) Tropic Thunder (2008) Up (2009) Up in the Air (2009) Waitress (2007) WALL·E (2008) Waltz with Bashir (2008) The Wrestler (2008) V for Vendetta (2005) Y tu mamá también (2001)
19 of my picks are comedies, and 9 are foreign films.
3 and a half were animated (Up, WALL·E, Waltz with Bashir and half of Avatar).
16 of them were nominated for Best Picture, and 4 of them won.
4 directors (Wong Kar-Wai, Michael Moore, the Coen Brothers and Alfonso Cuarón) made 2 on the list. Darren Aronofsky (The Fountain, Requiem for a Dream, The Wrestler) and Peter Jackson (each of The Lord of the Rings) made 3. Quentin Tarantino made 3 and a half. (Grindhouse, Kill Bill Vol. 1, Kill Bill Vol. 2, Inglourious Basterds).