I keep ongoing lists of these kind of things (see my RYM page in my signature)
Here is my top 100 of the decade:
1. Drive-By Truckers – Southern Rock Opera
2. Wilco – A Ghost is Born
3. Ryan Adams – Heartbreaker
4. Tom Waits –Orphans: Brawlers, Bawlers and Bastards
5. Okkervil River – Black Sheep Boy
6. My Morning Jacket – Z
7. Magnolia Electric Co.- What Comes After the Blues
8. Bob Dylan – Love and Theft
9. The White Stripes – Elephant
10. Neil Young & Crazy Horse – Greendale
11. Drive-By Truckers – Decoration Day
12. Beck – Sea Change
13. Black Keys – Rubber Factory
14. My Morning Jacket – Okonokos
15. Blitzen Trapper – Furr
16. Son Volt – American Central Dust
17. The Black Crowes – Before the Frost…
18. Reigning Sound – Love and Curses
19. The Hold Steady – Boys and Girls in America
20. Songs: Ohia - Songs: Ohia
21. Wilco – Yankee Hotel Foxtrot
22. The White Stripes – White Blood Cells
23. Calexico – Feast of Wire
24. Slobberbone – Everythingthing You Thought Was Right….
25. Magnolia Electric Co. – Josephine
26. Centro-Matic – Love You Just the Same
27. Sun Kil Moon – Ghosts of the Great Highway
28. Tom Waits - Alice
29. The Flaming Lips – Yoshimi Battles the Pink Robots
30. Gov’t Mule – Life Before Insanity
31. The Felice Brothers – Tonight at the Arizona
32. Bruce Springsteen – Magic
33. The Mars Volta – Frances the Mute
34. Exploding Hearts – Guitar Romantic
35. The Strokes – Is This It?
36. Gillian Welch – Time (the Revelator)
37. Drive-By Truckers – The Dirty South
38. The Dirtbombs - Ultraglide in Black
39. Okkervil River – The Stage Names
40. Reigning Sound – Too Much Guitar
41. Rush – Snakes and Arrows
42. Iron & Wine – The Sheppard’s Dog
43. The White Stripes – Icky Thump
44. James McMurty and the Heartless Bastards – Live in Aught-Three
45. Ryan Adams – 48 Hrs
46. Will Johnson – Vultures Await
47. Arcade Fire – Funeral
48. The National – Boxer
49. Bruce Springsteen – The Rising
50. Ryan Adams & The Cardinals – Cold Roses
51. The Raconteurs – Consolers of the Lonely
52. OutKast – Stankonia
53. Alejandro Escovedo – A Man Under the Influence
54. Mcclusky – Mcclusky Do Dallas
55. Nick Cave and the Bad Seeds – No More Shall We Part
56. Loretta Lynn – Van Lear Rose
57. The Avett Brothers – I and Love and You
58. Amy Winehouse – Back to Black
59. The Jayhawks – Rainy Day Music
60. Queens of the Stone Age – Rated R
61. Frank Turner – Love, Ire and Song
62. Patterson Hood – Murdering Oscar (and Other Love Songs)
63. Manic Street Preachers – Journal for Plague Lovers
64. Ryan Bingham – Mescalito
65. Steve Earle – Transcendental Blues
66. Lucero – Rebels, Rogues and Sworn Brothers
67. The Hold Steady – Stay Positive
68. Jenny Lewis with the Watson Twins – Rabbit Fur Coat
69. Sufjan Stevens – Illinois
70. The Compulsive Gamblers – Crystal Gazing Luck Amazing
71. The Flaming Lips – Embryonic
72. Stephen Malkmus – Real Emotional Trash
73. Spoon – Ga Ga Ga Ga Ga
74. Wilco – Kicking Television
75. Tom Waits – Blood Money
76. Drive-By Truckers – Brighter Than Creations Dark
77. The Black Keys - Thickfreakness
78. Gillian Welch – Soul Journey
79. Hayes Carll – Trouble in Mind
80. Marc Ford – Weary and Wired
81. Tool – Lateralus
82. Bon Iver – For Emma, Forever Ago
83. The Tallest Man on Earth – Shallow Grave
84. Okkervil River – The Stand Ins
85. Elvis Costello – Momofuku
86. The Dead Weather – Horehound
87. Madvillain – Madvillainy
88. At the Drive-In – Relationship of Command
89. Godspeed You! Black Emperor - Lift Yr. Skinny Fists…
90. Magnolia Electric Co. – Sojourner
91. Son Volt – The Search
92. Reigning Sound – Time Bomb High School
93. Wilco – Sky Blue Sky
94. The Mars Volta – De-Loused in the Comatorium
95. Modest Mouse – The Moon & Antarctica
96. Green Day – American Idiot
97. Dinosaur Jr – Farm
98. My Morning Jacket – It Still Moves
99. The Libertines – Up the Bracket
100. The Rolling Stones – A Bigger Bang