Fedor, easily.
Anderson Silva has too many losses from early on in his career, to very mediocre fighters on top of that.
Anderson also hasn't faced the best opponents. I mean, really.... look at the guys he beat since joining the UFC:
Chris Leben - Good fighter, but nowhere near great.
Rich Franklin x2 - These were very good wins, but nowhere near as impressive as Fedor's wins against Cro Cop, Big Nog, etc.
Travis Lutter - Joke.
Nate Marquardt - Known as a guy who can't win the big one.
Dan Henderson - Great win here, no denying that, but Henderson is best at Light Heavyweight, not Middleweight.
James Irvin - Joke.
Patrick Côté - Joke, plus one of the worst main events in UFC History.
Thales Leites - Joke, plus one of the worst main events in UFC History.
Forrest Griffin - Silva's greatest, most impressive performance to date, but Forrest isn't necessarily considered to be truly a great fighter at this point.
Damien Maia - Joke, plus one of the worst main events in UFC History.
Chael Sonnen - Great win for Silva.
Vitor Belfort - Good win, but Belfort didn't even deserve the shot at Silva. There's no way anyone could argue that Belfort was ever near the top of the heap in the Middleweight Division.
So, out of those, the wins against Sonnen, Griffin, Henderson, and Franklin are truly the only the fights worth praising Anderson on, and this is coming from a big Anderson Silva fan. The UFC's Middleweight Division was just too weak for far too long; it wasn't until Sonnen came along to where people could even start to take an interest to it.
Fedor Emelianenko, on the other hand, fought the absolute best in his division the entire decade. Even the UFC's best, since he would defeat the two guys who carried the UFC Heavyweight Division for years once they left the UFC in Andrei Arlovski and Tim Sylvia, and not only did he beat them, but he destroyed him. The only big Heavyweights Fedor didn't face from 2000-2009 were Randy Couture (which Fedor did everything in his power to do), and Josh Barnett (after years of ducking Fedor, he finally took a fight with him, only to fail a drug test). But that's it... he's always fought the best of the best in his division. Anderson Silva cannot say the same, since for a while the best competition in his division weren't in the UFC, and the top competition that was in the UFC, they just weren't that impressive.
Moreover, the question is who has had the better decade... name one Fedor fight that was boring? Does it exist? I don't think so. However, Anderson Silva is now infamous for his boring fights. You have to take into account that not only did Fedor have the better competition and the overall better record, but he had the more entertaining fights as well. Silva's terrible showings against Maia, Lietes, and Cote really hurt his case in this discussion, no matter how you look at it.
I would argue that when you look at the fighters who had the best decade, four names should come to mind: Fedor, Wanderlei Silva, GSP, and Anderson Silva (Liddell and Hughes would be considered, but their runs ended so awfully by the end of the decade that it wouldn't be right to include their names). And while you can make an argument for how you list 2-4, Fedor is indisputably #1.