Children of Men
As a movie fan, one of the best experiences is watching a movie you haven't seen in years and it still holding up 100%. If Children of Men isn't perfect, it's pretty close. It's probably the most accurate depiction on the near future, and I love how the technological advancements are subtle, so they're only set dressings and aren't in your face, trying to be a pivotal part of the movie. The nazi themes and the immigration issues are obviously just as relevant now - if not more so - than they were in 2006. I also like how it shows both extreme sides as being malefactors; the government is rounding up (and often killing) refugees, but the Fishes are just as willing to kill for their own egos and to use the first child born in the past two decades as propaganda. And Jasper is probably one of my favorite movie characters, period.
At the time, I thought the 2000s were a shit decade for movies, and even in hindsight, I haven't changed that opinion. If I had to rank my top handful of 2000s movies, they'd be:
Children of Men
Eternal Sunshine
Mulholland Drive
Lost in Translation
Those, IMO, are the only excellent movies of the decade. Everything else, like Memento, LotR, Donnie Darko, etc. are just "very good". I'd maybe consider adding Shawn of the Dead to the top list.