The AV Club and All Songs Considered both put together a best 50 of the aughts list. Combine the two and I've got half in my collection:
Animal Collective, Merriweather Post Pavilion (2009)
Arcade Fire, Funeral (2004)
Beck, Sea Change (2002)
Bon Iver, For Emma, Forever Ago (2008)
Clap Your Hands Say Yeah, Self Titled (2005)
Coldplay, A Rush Of Blood To The Head (2002)
Death Cab For Cutie, Transatlanticism (2003)
Interpol, Turn On The Bright Lights (2002)
LCD Soundsystem, Sound Of Silver (2007)
Midlake, The Trials Of Van Occupanther (2006)
Modest Mouse, The Moon & Antarctica (2000)
Neko Case, Fox Confessor Brings The Flood (2006)
New Pornographers, Mass Romantic (2000)
Phoenix, Wolfgang Amadeus Phoenix (2009)
Radiohead, In Rainbows (2007)
Radiohead, Kid A (2000)
Sigur Ros, ( ) (2002)
The Flaming Lips, Yoshimi Battles The Pink Robots (2002)
The Postal Service, Give Up (2003)
The Strokes, Is This It (2001)
The Swell Season, Once Soundtrack (2007)
The White Stripes, White Blood Cells (2001)
Various, O Brother, Where Art Thou? Soundtrack (2000)
Wilco, Yankee Hotel Foxtrot (2002)
Out of those my top three (at the moment) are Bon Iver, In Rainbows and LCD Soundsystem. Wilco is a close 4th but that's based on their whole catalog. A Ghost is Born is a better album in my mind even though YHF makes a better story.
