http://fishpork.com/2009/11/11/fishporks-100-favorite-tracks-of-the-2000s/

Sorry for the terrible formatting.

1 Panda Bear “Bros” (2007)
2 The Knife “We Share Our Mother’s Health” (2006)
3 Animal Collective “For Reverend Green” (2007)
4 Grizzly Bear “While You Wait For The Others” (2009)
5 The Knife “Heartbeats” (2003)
6 Grizzly Bear “The Knife” (2005)
7 LCD Soundsystem “Someone Great” (2007)
8 TV on the Radio “Staring at the Sun” (2003)
9 Crystal Castles “Crimewave” (2008)
10 Beirut “Ciloqut” (2007)
11 Thom Yorke “Harrowdown Hill
12 Animal Collective “Derek” (2007)
13 Nine Inch Nails “Me, I’m Not” (2007)
14 Beck “Lonesome Tears” (2002)
15 At The Drive-In “One Armed Scissor” (2004)
16 Animal Collective “Grass” (2005)
17 Deerhunter “Nothing Ever Happened” (2008)
18 Atlas Sound “Recent Bedroom” (2008)
19 Panda Bear “Comfy in Nautica” (2007)
20 System of a Down “Chop Suey” (2001)
21 Animal Collective “Peacebone” (2007)
22 Battles “Atlas” (2007)
23 Error “Jack the Ripper” (2004)
24 Enon “Pleasure and the Privilege”
25 Elliott Smith “Son of Sam” (2000)
26 Animal Collective “Did You See the Words” (2005)
27 The Knife “Marble House” (2006)
28 LCD Soundsystem “All My Friends” (2007)
29 Thom Yorke “Analyse” (2006)
30 The Flaming Lips “Ego Tripping at the Gates of Hell” (2002)
31 Girl Talk “Smash Your Head” (2006)
32 A Perfect Circle “Judith” (2000)
33 Radiohead “Idioteque” (2000)
34 Tapes N’ Tapes “Manitoba” (2006)
35 TV On The Radio “I Was A Lover” (2006)
36 Radiohead “Reckoner” (2007)
37 Fever Ray “Coconut” (2009)
38 Animal Collective “My Girls” (2009)
39 Built to Spill “Things Fall Apart” (2009)
40 Wilco “I’m Trying to Break Your Heart” (2002)
41 Modest Mouse “Tiny Cities Made of Ashes” (2000)
42 Animal Collective “Leaf House” (2004)
43 Modeselektor “Happy Birthday” (2007)
44 Arcade Fire “Wake Up” (2004)
45 Autolux “Blanket” (2004)
46 MGMT “Time to Pretend” (2007)
47 Built to Spill “Conventional Wisdom” (2006)
48 Wilco “Side With the Seeds” (2007)
49 Elliott Smith “Happiness/The Gondola Man” (2000)
50 Avey Tare “I’m Your Eagle Kisser” (2007)
51 Department of Eagles “Waves of Rye” (2008)
52 Animal Collective “Summertime Clothes” (2009)
53 Radiohead “2+2 = 5? (2003)
54 Dredg “Sang Real” (2005)
55 While Lies “Farewell to the Fairground” (2009)
56 Grizzly Bear “Ready, Able” (2009)
57 Matisyahu “King Without a Crown” (2005)
58 Modest Mouse “Paper Thin Walls” (2000)
59 Dillinger Escape Plan “When Good Dogs Do Bad Things” (2002)
60 Elliott Smith “Twilight” (2004)
61 Deerhunter “Flourescent Grey” (2007)
62 Holy Fuck “Lovely Allen” (2007)
63 LCD Soundsystem “Never As Tired As When I’m Waking Up” (2006)
64 The Notwist “Boneless (Panda Bear Remix)” (2008)
65 Liars “Nothing Is Ever Lost or Can Be Lost My Science Friend” (2004)
66 The Mars Volta “Inertiatic E.S.P." (2003)
67 The Notwist “Solitaire” (2002)
68 Of Montreal “The Past is a Grotesque Animal” (2007)
69 Queens of the Stone Age “Tangled Up in Plaid” (2005)
70 Radiohead “Jigsaw Falling Into Place” (2007)
71 Saul Williams “Raised To Be Lowered” (2007)
72 Autolux “Great Days for the Passenger Element” (2004)
73 Sigur Ros “Untitled 8? (2002)
74 Yeah, Yeah, Yeahs “Maps” (2003)
75 Portishead “Threads” (2008)
76 Sufjan Stevens “Chicago” (2005)
77 Ugly Casanova “Things I Don’t Remember” (2002)
78 Animal Collective “Brothersport” (2009)
79 Radiohead “Pyramid Song” (2001)
80 Nine Inch Nails “Only” (2005)
81 El-P “Flyentology” (2007)
82 Queens of the Stone Age “No One Knows” (2002)
83 Ghostface Killah “Shakey Dog” (2006)
84 Modest Mouse “Missed the Boat” (2007)
85 UNKLE “Persons and Machinery” (2007)
86 Amon Tobin “Verbal” (2002)
87 The White Stripes “Denial Twist” (2005)
88 Tomahawk “Captain Midnight” (2003)
89 Modest Mouse “Bukowski” (2004)
90 Sigur Ros “Hoppipolia” (2005)
92 Fuck Buttons “Sweet Love For Planet Earth” (2008)
93 Bon Iver “Skinny Love” (2008)
94 Built to Spill “In Your Mind” (2001)
95 The White Stripes “Icky Thump” (2007)
96 Does It Offend You, Yeah? “We Are Rockstars” (2008)
97 Dub Trio “Not Alone” (2006)
98 Modest Mouse “The World At Large”
99 The Walkmen “In the New Year” (2008)
100 Nine Inch Nails “The Great Destroyer (Modwheelmood Remix)” (2007)

I give this list credit for voting for some unusual songs, but it is way too indie-focused and includes too many songs by a few artists (Animal Collective, Grizzly Bear, and The Knife especially). There were some great hip-hop and pop songs this decade too, which this list entirely ignores. At least you can't say it's a Pitchfork-copier.