Let's start with two of the more objective resources: Rateyourmusic.com and Metacritic.com.
Rateyourmusic allows users to do just that. No critics, no experts; just the fans. Because of the democratically representative nature of this format, it's perhaps one of the most pure barometers of what's good in music. Of course the flaw is in the sampling method: the voting population consists of people a.) in the know and b.) who care enough to do it. Still, there's no one genre that dominates the list, and most reputable artists can boast representation (I'm particularly proud that Tom Waits' masterpiece Rain Dogs is the 5th ranked album of the 80s.)
As for the 00s: The top album is Radiohead's Kid A, not an uncommon critical choice and perhaps only slightly less common as the popular choice. Arcade Fire's Funeral is second, followed by Godspeed You Black Emperor's Lift Yr. Skinny Fists Like Antennas to Heaven. Wilco's Yankee Hotel Foxtrot is #4. The rest of the list is here. Radiohead shows up again at 13 (In Rainbows) and 32 (Amnesiac). Only Hail to the Thief didn't make the top 100, which is surprising to me. I'd put it ahead of Amnesiac, but it seems not to have aged as well as most other albums to most. It should be noted that no 2009 albums have been factored in to the list quite yet. One more Radiohead tidbit: They also netted the best album of the 90s with OK Computer, with The Bends coming it at #9.
Metacritic gives its scores based on an aggregate of critical ratings from a number of publications. However, they prominently feature reissues (always ratings boons) and list them in the company of new releases. The site only began in 2001, so its "All Time" ratings list is effectively the best of the decade. With a cumulative rating of 97/100, Brian Wilson's Smile ties with Loretta Lynn's Van Lear Rose as the most critically acclaimed new release of the decade. The shortcoming here is that there are certain artists who earn critical praise based on staying power alone. Not to mention a well-liked country legend produced by a young rocker (Jack White, in this case) is the kind of storyline that critics devour. And Brian Wilson's long-shelved masterwork was a can't-miss.
Moving on to some specific web and print publications' rankings:
Pitchfork: Radiohead - Kid A
Did anyone not see this coming? Pitchfork's well-document love affair with Radiohead has spanned two decades now. To their credit, their picks mirror Rateyourmusic's, so maybe they do have their fingers on the pulse of good taste.
AV Club: The White Stripes - White Blood Cells
Jack and Meg were undoubtedly a powerhouse in the 00s, and there's no denying that their breakout disc is a stellar album. "Dead Leaves On the Dirty Ground," "Hotel Yorba," "Fell In Love With a Girl," and "We're Going To Be Friends" are songs even most casual music fans would recognize...and, wouldn't you know it, they're actually good songs. The snob in me says I prefer Elephant and actually Icky Thump, but song for song, White Blood Cells has to take it as far as the Stripes go. Tops in the 00s? Sure, why not.
NME: The Strokes - Is This It
While it's true Is This It is already being referred to as an era-defining record, it's hard to argue that such a label means much anymore. Musical fads come and go quicker than ever these days, right? But to be fair, the Strokes had a noticeable cultural impact that extended well beyond the speakers. Especially noteworthy: Every lanky 15 year old growing a poofy Jewfro; the temporary extinction of the upstrum; an emphasis on the band naming formula of (The + plural noun). And, sure, the record is pretty damned good.
Paste: Sufjan Stevens - Come On, Feel The Illinoise
Paste often wears it's favorite bands on its sleeves, so it's no surprise Sufjan snagged their top spot. But again, it's a fairly epic release and the gold standard of 00s indie folk. His sprawling arrangements paired with his meek voice convey that relatable feeling of a small presence in a big world.
Uncut Magazine: The White Stripes - White Blood Cells
Another one for the Stripes' breakthrough, this time from the well-known British music mag.
SnobMusic.com: Hold Steady - Boys and Girls In America
The Hold Steady's third album is an excellent choice for best of the decade because it's such a vivid countercultural snapshot. Craig Finn's lyrics speak of coming-of-age youth in America the way Springsteen did in the 70s. Finn's earnest tales of druggie parties, faith crises, and self realization resound so purely with his target audience of literate rock disciples that he's been cast in a "Rock Messiah" role that surely makes him snicker. But nevertheless, the songs that make up Boys and Girls--and the perfect flow they create--is a thing to behold. "You Can Make Him Like You" might be the song of the 00s, with its brilliant lyrics, slathered irony, crowd-surfing above the rolling piano, guitars and drums.
eMusic.com: The Strokes - Is This It
Another one for the Strokes' debut. Since I've already covered it, I'd like to take this opportunity to praise their second album, Room on Fire. It's a little less revolutionary, but there are some essential tunes on it, especially the all-kinds-of-ass-kicking "Reptilia".
"Sure," you might be saying, arms folded and Frito crumbs dusting your keyboard, "HSW can critique other lists but don't have the cajones to make their own!" Again, I don't feel nearly qualified enough to be able to make a comprehensive list. Remember that these other publications have a team of music critics who, between them, have probably heard just about all that's worth hearing.
But you've convinced me, guy that probably doesn't exist. Here now, I present The HSW Invalid as Hell and Really Just A List of Favorites Top 20 Records of the 2000s:
20. Grizzly Bear - VeckatimestThe unofficial HSW best of the 00s list...happy? I hope you had a nice decade, and many happy returns in the next one.
19. The Shins - Chutes to Narrow
18. Ryan Adams - Love Is Hell
17. My Morning Jacket - Z
16. The National - Alligator
15. Drive-By Truckers - Decoration Day
14. Iron and Wine - Shepherd's Dog
13. M. Ward - Post War
12. Radiohead - Kid A
11. Wilco - A Ghost Is Born
10. Band of Horses - Everything All the Time
9. Spoon - Ga Ga Ga Ga Ga
8. Radiohead - In Rainbows
7. Gillian Welch - Time (The Revelator)
6. Bright Eyes - I'm Wide Awake and It's Morning
5. Arcade Fire - Funeral
4. The Decemberists - Picaresque
3. Sun Kil Moon - Ghosts of the Great Highway
2. The Hold Steady - Boys and Girls in America
1. Wilco - Yankee Hotel Foxtrot