Agree with many of these. I'll throw one out there that moves in a slightly different direction:
The Shins - New Slang (or the entire soundtrack from Garden State, really).
There was also the fairly shortlived British invasion wave that peaked during the middle of the decade. Ohayou mentioned Franz Ferdinand already, but other examples include Keane - Only Somewhere We Know and the Kooks - Naive. And while we've all mostly blocked them from our collective consciousnesses, it's hard to discuss 2000s music without mentioning Coldplay (at least until they decided to cease to be a rock band).
Edit:
Wait. No. Scrap all of that. The Most 2000s song is My Chemical Romance - Welcome to the Black Parade.