More a personal favourites list, rather than a "best of"... in chronological order:
Radiohead - Kid A (2000)
Still comes on like an unexpected handbreak turn. Initially inpenetrable, but the fruits it bares are most rewarding.
U2 - All That You Can't Leave Behind (2000)
Coldplay probably wouldn't have maintained a career if this album wasn't released to such success and acclaim. Unfortunately, it's been taken apart, broken down and re created like a bad facsimilie by countless other bands since.
Queens of the Stone Age - Restricted (2000)
Still their best record IMO. 'Songs For The Deaf' was darker, more sprawling, messier, but 'Restricted' is more fun and has better songs on a whole. Again, my opinion only.
You Am I - Dress Me Slowly (2001)
Australia's best rock band make a concerted effort to write songs that would finally assure them the mainstream success they deserve. They fail. 2 years later, Jet rip them off with a quarter of the talent, less lyrical panache and more AC/DC influences to worldwide success and acclaim. There is no God.
Avalanches - Since I Left You(2001)
The most inventive and innovative use of samples I've ever heard on record. Meanders a little towards the end, but stuff like 'Frontier Pyschiatrist' are stone cold mind blowing classics.
Eels - Souljacker (2001)
My favourite Eels record : vicious songs about love, lust, violence and incest. E appeals to me most when he's taking the dumb rock stance.
David Bowie - Heathen (2002)
Enough has been said about this record on these boards, I really don't need to go into it any further - but I will say, that in terms of songwriting and craft, this is Daddy's most consistant record in forever.
Red Hot Chili Peppers - By The Way (2002)
Sure to take some stick for this one, but this band was a very important part of my youth. A very rich and diverse album that my friends and I dismissed at the time for being too mellow. Of course, now, I appreciate the textures and inventiveness much more and the harmonic interplay between Keidis and Frusciante is one of the key joys of this record.
Coldplay - A Rush Of Blood To The Head (2002)
Don't hate me Adam, but this is such a finely crafted pop record - even if the U2 influence is so blatant. But U2 were still cool in 2002, so it was OK.
Kings Of Leon - Aha Shake Heartbreak (2003)
Contender for the rock album of the decade IMO. All booze, sex and rock n roll, without even a whiff of their present stadium-rock pretensions.
Nick Cave & The Bad Seeds - Abattoir Blues/The Lyre of Orpheus (2004)
My formal introduction to Nick Cave. One of the few albums I've played so much that I actually wore out and had to purchase again. The perfect balance between the noisy rock and tender ballads Nicky does so well.
Arcade Fire - Funeral (2004)
I got this album due to Bowie's raving about them. I was suitably impressed.
The Futureheads - The Futureheads (2004)
Perhaps the most forgettable album of the bunch, but these guys connected with me more than Franz Ferdinand or The Strokes or The Libertines at the time. Unfortunately, their schtick grew tiresome after one record.
The White Stripes - Get Behind Me Satan (2005)
The most sonically interesting White Stripes record IMO. Jack White is the sole genius that future generations will refer to from the 00s.
Franz Ferdinand - You Could Have It So Much Better (2005)
I liked the songs on this one better than Franz' debut - particularly 'The Fallen', the title track and 'The Outsiders'. Gets a bit self concious in the middle, but ends strongly.
Bloc Party - Silent Alarm (2005)
The most innovative rock record in recent memory. Nothing they've done since has interested me though.
Neil Young - Living With War (2006)
A cutting memento of the Bush administration. None of the younger groups cared enough to focus their anger into record. Maybe Green Day, but Green Day suck dude.
Amy Winehouse - Back To Black (2006)
Finally! A female pop star with substance! Unfortunately, she had too many substances and it wouldn't surprise me if she never made another record.
Bruce Springsteen - Magic (2007)
The Boss' great re-embracing of pop music. Doesn't have the political edge that 'The Rising' had, but is a more concise record where every cut is prime Boss.
Radiohead - In Rainbows (2007)
The album that 'Hail To The Thief' aspired to be, but fell short of because it was too long winded. Probably their best album.
Nick Cave and the Bad Seeds - Dig Lazarus Dig!!! (2008)
Grinderman revitalised Nicky with a lust insatiable. He carries it through here to what could be the best Bad Seeds album yet.
R.E.M. - Accelerate (2008)
Just when R.E.M. looked done and dusted, seamlessly slipping into the streams of MOR adult contemporary, they hit back with an album as good as 'Document'. The rock album 'Monster' should have been.
Vampire Weekend - Vampire Weekend (2008)
Interesting instrumentation, quirky song structures... a breath of fresh air.
The Raconteurs - Consolers Of The Lonely (2008)
Jack White's rock n roll opus. It's too long, but the thrills and (Carolina) drama are plenty.
Bob Dylan - Together Through Life (2009)
Could have been any 3 of his albums in this decade, but the Tex-Mex instrumentation on this record is a real kick for me, after the smoke screen atmopsherics of the previous 2.
I used to be with it, but then they changed what "it" was. Now, what I'm with isn't it, and what's "it" seems weird and scary to me.