i'm thinking the top of the list looks something like this:
1. The Marshall Mathers LP (2000) - Eminem
2. Stankonia (2000) - OutKast
3. The College Dropout (2004) - Kanye West
4. The Blueprint (2001) - Jay-Z
5. Speakerboxxx/The Love Below (2003) - OutKast
6. Kid A (2000) - Radiohead
7. American Idiot (2004) - Green Day
8. Late Registration (2005) - Kanye West
9. Lil Wayne (2008) - Tha Carter III*
10. FutureSex/LoveSounds (2006) - Justin Timberlake*
two things i've noticed so far, the great female artists of the decade are far more singles-oriented (i'm really unsure where to rank Dangerously in Love or any of Britney's albums). also, the sales for albums in the second half of the decade dipped dramatically (probably a combination of factors, the most important being the continued rise of the internet and file sharing).
Is This It by The Strokes shouldn't be out of the Top 10. It's influence/musical impact is so massive that it cannot be justified to see it lower than 10.
the 10th spot is the most difficult for me. because that top 8 i think its pretty much locked in and i also see Wayne being a solid number 9 choice. but i just don't know about 10. there are massively popular albums like Oops I Did It Again, Hybrid Theory, and No Strings Attached that lack musical impact. there are highly praised albums like Funeral, Is This It, and Yankee Hotel Foxtrot that lack any real popularity outside of small corners of the internet (Is This It had a small amount of mainstream popularity and YHF has seen its popularity grow a bit over the years imo, but it doesnt compare to the top albums on this list). then you have albums who do well in both musical impact and popularity like FutureSex/LoveSounds, Toxicity, A Rush of Blood to the Head, Elephant, and The Black Album. its a tricky situation.
what i want to be careful about is not getting swept up in acclaimedmusic's rankings, because of the indie rock bias that comes with compiling that many online publications. its a good source to use, but not a perfect one. i think its important to remember that what is big on the internet and within indie rock circles is not always that big overall. that's not to say that Is This It wasn't a great album, because it definitely was. but FutureSex/LoveSounds and The Black Album weren't just big in one corner of the rock world, they were big on a massive scale.