To start this off, here's 5 that just missed out on the final list
Arctic Monkeys "I Bet You Look Good on the Dancefloor" (2005)
I never quite got on board with Alex Turner as the best thing to happen to British alternative rock, but for about three minutes right at the start of his bid for the title it was worth believing the hype. Ignoring a few too-clever-by-half lyrics (the strained reference to Rio mostly) this was among the best first singles released this decade, and as a result everything after that fell into its shadow.
Hanson "If Only" (2000)
I'll freely admit to lumping them in with Britney and Backstreet back in the "Mmmmbop" days, but deep down I think I always realized they didn't fit in there. The two singles from their sophomore album pretty much cleared that up, and "If Only" especially stands as one of the best pure pop songs of the early decade. Of course the public wanted another "Mmmbop" and this went nowhere, but the odd time that I hear it it always manages to make me smile.
Janet Jackson "Feedback" (2008)
The 00s weren't Janet's best decade. Sure she had a few mega hits at the beginning of the decade, but even those were disappointing to me, especially after The Velvet Rope's more personal and much more harsh material. Thus when "Feedback" broke out last year it was one of the most pleasantly surprising singles in a while. The lyrics may be pretty standard, but the production is the main attraction here. Futuristic yet retro, full of odd little tics (the distortion that envelops the whole track during the second verse is particularly inspired) and easily the most satisfying stuff Janet had to work with all decade. It's like a spiritual cousin to "If", and all the better for it.
Lil' Wayne "A Milli" (2008)
Lil' Wayne is probably the most interesting pop personality of the 00s, one who fumbles more often than he hits but is never boring when he does it at least. This is the most theoretically annoying song ever, but somehow the combination of incessant repetition of the title as the beat, volume variance of the master track replacing actual dynamics and Lil' Wayne being his usual self works like a charm. I'm not gonna try to figure out why for fear of going insane in the process.
Ying Yang Twins "Wait (The Whisper Song)" (2005)
Has there ever been a pop hit so unambiguously dirty? I mean, Prince was more subtle than this and he's fucking Prince.