I will admit that I'm put off by the presence of two Radiohead songs in the top ten, but I am a very biased man, admittedly. However, at least neither of them are from Kid A or Amnesiac, so I'll refrain from getting as harsh as I could get. 😄
Outside of that, though, a very interesting melange of stuff. My favorites here are 24, 32 (proof positive that DJ Paul and Juicy J were two of the most musically forward-thinking producers in all of hip-hop), and 87. 95 is a pretty nice tune, as well, even though I'm not a huge Coldplay guy (I do still prefer them to 2000s Radiohead by far, however, but anyway...).
Some artists that I would have personally included somewhere on here are Eminem, System of a Down, Green Day, and Kanye West. Eminem is my favorite rapper of all time, SOAD are my favorite rock band of the 2000s, Green Day are one of my favorite bands of all time, and Kanye's early work remains great (recent shenanigans notwithstanding).
"doubles from 4 albums in just the top 15"
That's because Vespertine and In Rainbows are both flawless masterpieces. Without the restriction the top 20 would consist largely of songs from both those albums
Cool that you finally posted, interesting picks. It's my favorite decade and my top 35 would be 1. Arriving Somewhere but Not Here by Porcupine Tree 2. The Stars Are Projectors 3. Reflection by Tool 4. Bleak by Opeth 5. Shadow of Our Pale Companion 6. Eos by Ulver 7. Wayfarer by Kayo Dot 8. Wings for Marie (10,000 Days Pt. 2) 9. Untitled #3 by Sigur Ros 10. Black Gold by Foals 11. How to Disappear Completely 12. Falling Snow by Agalloch 13. Anesthetize by Porcupine Tree 14. Blackwater Park 15. Lateralus 16. Ghost of Perdition 17. The Leper Affinity 18. Girl with a Watering Can 19. Reckoner by Radiohead 20. Track one on album Part the Second 21. Garden of Light by Isis 22. .3 by Porcupine Tree 23. Shadows of the Sun 24. Mistaken for Strangers 25. The Manifold Curiosity 26. Apartment Story 27. Weird Fishes/Arpeggi 28. Breathe Me by Sia 29. Gong by Sigur Ros 30. Ghost Key by Isis 31. No Cars Go by Arcade Fire 32. Fake Empire 33. Life Like Weeds 34. Geese of Beverly Road 35. All I Need by Radiohead.