In order to avoid repeating bands and artists, I have only ranked my favorite album for each act, and have listed other albums that probably would have made the list under a "See also:" section. I also threw album covers and blurbs for the top 20.
Happy New Year and may the next decade be even greater!
MATT DUFFY’S ALBUMS OF THE DECADE
2000 - 2009
2000 - 2009
50. HOT CHIP - Made In The Dark
49. FLEET FOXES – Fleet Foxes
48. SERVICIO DE LAVANDERÍA - Shakira
47. GIVE UP - Postal Service
46. JUSTIFIED - Justin Timberlake
45. LOVE AND THEFT - Bob Dylan
44. IN THE ZONE - Britney Spears
43. ¡SONIDO AMAZONICO! - Chicha Libre
42. SPIDERMAN OF THE RINGS - Dan Deacon
41. DISCOVERY - Daft Punk
40. RADIO BEMBA SOUND SYSTEM - Manu Chao
39. FLYING CLUB CUP - Beirut
38. BLACK HOLES & REVELATIONS - Muse
37. COME AWAY WITH ME - Nora Jones
36. MERRYWEATHER POST PAVILION - Animal Collective
(See also: FEELS)
35. LET GO - Avril Lavigne
34. I AM NOT AFRAID OF YOU AND I WILL BEAT YOUR ASS - Yo La Tengo
33. SMILE - Brian Wilson
32. RAISING SAND - Robert Plant and Alison Krauss
31. GREEN ALBUM - Weezer
30. VAMPIRE WEEKEND 29. BLACKLISTED - Neko Case
28. UNCLASSIFIED - Robert Randolph & The Family Band
27. SOULJACKER - Eels
26. CHANGING HORSES - Ben Kweller
(See also: ON MY WAY)
25. PERMISSION TO LAND - The Darkness
24. LOOK INTO THE EYEBALL - David Byrne
(See also: EVERYTHING THAT HAPPENS WILL HAPPEN TODAY, GROWN BACKWARDS)
23. THE FORGOTTEN ARM - Aimee Mann
(See also: LOST IN SPACE, BACHELOR No. 2)
22. CHUTES TOO NARROW - Shins
(See also: O, INVERTED WORLD!)
21. SPEAKERBOXXX / THE LOVE BELOW - Outkast
(See also: STANKONIA)

Close your eyes and try to remember how much this album blew your mind the first time you heard it.
(See also: FIGHT TEST EP, AT WAR WITH THE MYSTICS)

I generally hate actress-turned-singer albums, but this one really works. By the way, M. Ward is obviously completely in love with her.

I was never a huge Pavement fan, so the fact that this album grew on me so much caught me off guard.

Those White Stripes albums are all basically the same, but this one has “Ball And A Biscuit.” Cheers, White Stripes. Couldn’t have done the decade without you!
(See also: DE STIJL, WHITE BLOOD CELLS, GET BEHIND ME SATAN)

The album that saved rock music... again. Poor, pathetic rock. All hype surrounding this band was well-deserved, and they delivered on it with Neon Bible a few years later -- also, a great album. Crank up the volume on “Intervention” and I promise you will see God.
(See also: NEON BIBLE)

It’s real heavy, but at least he went out with his strongest work since Mr. Bad Example. R.I.P. (See also: LIFE’LL KILL YA, MY RIDE’S HERE)

I think of it as the fourth volume of 69 Love Songs. I cried the first time I heard “I Don’t Love You Any More.” That guy Merritt can really write!
(See also: DISTORTION)

I think we can all agree it was a great album. The other two were more of the same -- so, if you liked Is This It?, logic dictates you like the others also.
(See also: ROOM ON FIRE, FIRST IMPRESSIONS OF EARTH)

Good-old, sentimental, Mutations-style Beck. Information (real drums!) is great, too -- a very close second. The other albums from this decade were pretty standard Beck fare... Güero has some good tunes.
(See also: THE INFORMATION, GÜERO)

I can’t lie -- I love this album and listened to it many times in the last decade. What a tragedy that the predominantly non-autistic CD-buying audience dismissed it as a cult/novelty follow-up to Transformed Man (but who could blame them?). Shatner is poignant, fiery, vulnerable, hilarious, and beautifully complemented by Ben Folds’ musical arrangements and an all-star cast of guest vocalists.

Few bands ever achieve the cohesion required to produce the living studio alchemy heard here: a sonic journey through corny piano riffs, murky forests of noise, and some truly righteous jams. Tweedy channels John Lennon in his songwriting and vocals... his guitar is wild and otherworldly. Sky Blue Sky is probably the better album, but the raw personality of Ghost Is Born appeals to me more.
(See also: SKY BLUE SKY, YANKEE HOTEL FOXTROT)

Credit U2 for doing their best imitation of themselves here. Don’t call it a comeback. It’s just Joshua Tree II, and let the ‘90s be stricken from the record. So what if they gave up on experimentation and growth? The songs are over-the-top, broad, sweeping, anthemic and cheesy. This from any other band would be intolerable, but because they’re U2, they pull it off.
(See also: NO LINE ON THE HORIZON, HOW TO DISMANTLE AN ATOMIC BOMB)

I had to have Elliott Smith on the list. And I like Figure 8 as much as the next guy -- but, man, it sure is wussy. Basement On A Hill, on the other hand, is edgy, crunchy, and much more fun to listen to. Ironically, it might never have sounded like it does if E.S. had lived to see its release. R.I.P.
(See also: FIGURE 8, NEW MOON)

Undoubtedly one of the greatest lyrical geniuses of our time, this was my personal favorite of the great three-album oeuvre which also includes Slim Shady and Marshall Mathers.
(See also: THE MARSHALL MATHERS LP, ENCORE)

Musically, it’s a hard-hitting ‘70s throwback prog epic that opens all the stops. Then there’s the plot... sure, maybe the supernatural/tragic/Victorian theme doesn’t appeal to everybody -- but how many other supernatural/tragic/Victorian folk operas are there?
(See also: THE CRANE WIFE, PICARESQUE, CASTAWAYS & CUTOUTS)

A classic-rock tribute with a modern psychedelic twist, by the reincarnated Beta Band. The jams are homeruns, the slower bits brim with heart and soul, and everything flows together. So what if it runs a little long? “I am a robot man...”
(See also: LUNA)

I was shocked that this album didn’t make it onto more (read: all) of the mainstream “Top Album” lists. The production is intricate and flawless. Every song is a gem, even if Folds’ songwriting is real sappy at times. Still... I never get tired of listening to it.
(See also: BEN FOLDS LIVE, SONGS FOR SILVERMAN)

In Jim Chidley’s words, “The two sweetest sounds in the world are Knopfler’s guitar and Emmylou Harris’ voice.” I bet the songs would still be great even in the hands of complete hacks. Extra points for many fine solo albums by both artists, esp. Knopfler’s Shangri-La.
(See also: REAL LIVE ROADRUNNING) (See also: Knopfler: SHANGRI-LA, THE RAGPICKER’S DREAM, KILL TO GET CRIMSON, SAILING TO PHILADELPHIA, GET LUCKY) (See also: Harris: RED DIRT GIRL, STUMBLE INTO GRACE)

Hail To The Thief is the best one, but Amnesiac meant more to me personally. The reasoning behind my unorthodoxed ranking of these albums is fodder for another post, perhaps.

A true masterpiece pop album. Every song is brilliant. The structure and flow of the album are perfect. The band is at the peak of their talents: writing-wise, performance-wise and production-wise. And you can sing along to the whole thing! Full marks in all categories. Congrats for being number one, Guster!
(See also: GANGING UP ON THE SUN)