Top 100 of the 2000s

In list form, sans descriptions:

Top 20:

Adaptation (2002)

Almost Famous (2000)

American Psycho (2000)

Angels in America (2003)

The Assassination of Jesse James (2007)

Bright Star (2009)

Brokeback Mountain (2005)

Children of Men (2006)

Eternal Sunshine of the Spotless Mind (2004)

The Fall (2008)

Gosford Park (2001)

The Hurt Locker (2009)

In the Bedroom (2001)

LotR (2001, 2002, 2003)

Moulin Rouge (2001)

The New World (2005)

Pan’s Labyrinth (2007)

V for Vendetta (2005)

The Wind that Shakes the Barley (2007)

Zodiac (2007)

20-40:

Atonement (2007)

Chicago (2002)

The Constant Gardener (2005)

Departed (2006)

The Escapist (2008)

Frost/Nixon (2008)

Good Night and Good Luck (2005)

Hard Candy (2006)

The Hours (2002)

In Bruges (2008)

Inglourious Basterds (2009)

Last King of Scotland (2006)

Memento (2001)

Milk (2008)

Moon (2009)

No Country for Old Men (2007)

Painted Veil (2006)

Persepolis (2007)

Slumdog Millionaire (2008)

The Triplets of Belleville (2003)

40-60:
28 Days Later (2003)
Best in Show (2000)
The Bourne Identity (2002)
Brothers (2009)
The Brothers Bloom (2009)
Casino Royale (2006)
District 9 (2009)
Fantastic Mr. Fox (2009)
Finding Nemo (2003)
Hedwig and the Angry Inch (2001)
Lars and the Real Girl (2007)
Let the Right One In (2008)
Little Miss Sunshine (2006)
The Magdalene Sisters (2003)
The Motorcycle Diaries (2004)
Pride and Prejudice (2005)
The Royal Tennenbaums (2001)
Secretary (2002)
Waltz with Bashir (2008)
Watchmen (2009)

60-80:
Across the Universe (2007)
Batman Begins (2005)
Brick (2006)
The Damned United (2009)
Gone Baby Gone (2007)
I heart Huckabees (2004)
In the Loop (2009)
King Kong (2005)
Lost in Translation (2003)
Mirrormask (2005)
The Prestige (2006)
Rescue Dawn (2007)
Shattered Glass (2003)
Snow Angels (2008)
Sunshine (2007)
Sweeney Todd (2007)
Thirteen (2003)
Whale Rider (2003)
Winged Migration (2003)
Y Tu Mama Tambien (2002)

80- 100:
A Mighty Heart (2007)
Catch Me if You Can (2002)
Cloverfield (2008)
The Fountain (2006)
House of Flying Daggers (2004)
Howl’s Moving Castle (2005)
I'm Not There (2007)
Inside Man (2006)
Japanese Story (2003)
Kingdom of Heaven (2006)
Kinsey (2004)
Marie Antoinette (2006)
Monster (2003)
Mulholland Drive (2001)
Perfume: the story of a murderer (2006)
The Queen (2006)
Stardust (2007)
Wet Hot American Summer (2001)
X2 (2003)
Young Adam (2003)

Honorable mentions:
Wristcutters: A Love Story
Igby Goes Down
Kiss kiss bang bang
The Lookout
Grindhouse
Wanted
Sin City
Kill Bill
Lagaan: Once Upon a Time in India

Saw too late to make the list, but otherwise would be on there:
The Imaginarium of Doctor Parnassus
A Single Man
Fish Tank