I like this list better then your year one, but yeah, you are lying to yourself about Wilco man, give in!
Also, Andrew Peterson's Behold the Lamb is so dang good, I left it out of my list just because it's "Christmas album" status, even though it is so much more.
Here is mine.
1. Sufjan Stevens – Illinois
2. Wilco – Yankee Hotel Foxtrot
3. Over the Rhine – Ohio
4. Radiohead – In Rainbows
5. Gillian Welch – Time (the Revolator)
6. Ryan Adams – Cold Roses
7. TV on the Radio – Dear, Science
8. The Shins – Winching the Night Away
9. The Decemberists – Picaresque
10. Arcade Fire – Neon Bible
11. Elliott Smith – From a Basement on a Hill
12. Iron & Wine – Our Endless Numbered Days
13. Postal Service – Give Up
14. Coldplay – Paracutes
15. Flaming Lips – Yoshimi Battles the Pink Robots
16. Fleet Foxes – Fleet Foxes
17. Radiohead – Amnesiac
18. Danielson – Ships
19. Interpol – Antics
20. Sigur Ros – Takk
21. Ryan Adams – Heartbreaker
22. Phoenix – Wolfgang Amadeus
23. Neko Case – Foxconfessor Brings the Flood
24. Kings of Convince – Riot on the Empty Streets
25. Johnny Cash – American IV
And because I felt like I was giving the shaft to so many amazing albums, here are the next 25.
26. Bright Eyes – I’m Wide Awake It’s Morning
27. Spoon – Gimmie Fiction
28. Andrew Bird – Armchair Apocrypha
29. U2 – All That You Can’t Leave Behind
30. The Decemberists – Crane Wife
31. Nada Surf – Let Go
32. New Pornographers – Challangers
33. The Shins – Cutes To Narrow
34. Derek Webb – Stockholm Syndrome
35. Starflyer 59 – Dail M
36. Wilco – A Ghost Is Born
37. Rosie Thomas – These Friends of Mine
38. Son Lux – At War with Walls and Mazes
39. U2 – No Line on the Horizon
40. Son Volt – Okemah and the Melody of Riot
41. David Gray – White Ladder
42. Death Cab for Cutie – Transatlanticism
43. Jars of Clay – Good Monsters
44. Radiohead – Kid A
45. Jenny Lewis – Rabbit Fur Coat
46. Modest Mouse – Good News of People Who Love Bad News
47. Switchfoot – Learning to Breathe
48. Midlake – The Trials Of Van Occupanther
49. Fire Theft – Fire Theft
50. Elbow – Leaders of the Free World
Really, consider mine a top 5 list, with a lot of ties.