NME has posted their top 150 tracks of the past 15 years. It's an interesting list, in part, because of how badly the last two decades are underrepresented in Rolling Stones top 500 song list, even in the 2010 update. As one might expect, it's overly dominated by British guitar bands, especially ones that were edgy enough to stay off the US pop charts, but not edgy enough to stay off the UK pop charts.
Among the top 10, we find the Libertines (not in the Rolling Stones top 500), the Verve (#392 RS greatest songs of all time), Amy Winehouse (RS #194), Hot Chip (not on RS list), The White Stripes (#286 RS with a different song), The Killers (not on the RS list), The Strokes (RS #478), Outkast (RS #182), Arcade Fire (not on the RS list), and Radiohead (#257 on the RS list). I was surprised the Arctic Monkeys didn't make the top 10 for NME, but they're right there at #11. They don't make the RS list. They should.
Gnarls Barkley's "Crazy" the only song on the RS top 500 from the last 15 years (coming in at #100 no less) is at #32 on the NME list. So the fair comparison here is that RS puts Crazy at #1 for the last 15 years vs. NME putting it at #32. It was at #27 on my own list of the top 300 of the 2000s, but most of the songs and artists ahead of it aren't on either the NME or RS lists. If we restrict to the sorts of artists that RS and NME care about, I think RS came closer to getting that one right ('cuz you know there's a right and wrong here, right?).
The NME webpage is nice if you want links to youtube videos and you want to view it as a countdown ten songs at a time. If you want to skim the list with fewer clicks, it's available in more of a list format at Vinyl Surrender.