I'm not able to come up with a list of ten; would be more likely to be twenty or so. But what I feel would have a place amongst the top ten would be Donnie Darko.
Thanks Trident.
It doesn't have to be ten. I must admit my ten could have been a twenty, though it was interesting cutting them down on whatever criteria I used.
Pop up your twenty if you want to. In the New Year I might look at the lists and compile a top five or so of the titles that keep being cited here.
You asked for it... 
Ok, so be it. I won't bother to rank them, so order is mostly by chance:
Quantum of Solace - For no other reason than the producers being bold and brave enough to follow up their own masterstroke with a very experimental yet for me still satisfying entry.
The Last King of Scotland - For showing a rare close-up of a mass murderer. A stunning Whitaker.
Hotel Rwanda - For showing how common mass murder really is when it get's its chance. And for showing how ordinary courage can be, if it just get's the same chance. Cheadle impressed me just as much as Whitaker in TLKOS.
Match Point - Because I simply love Scarlett Johansson's character in this one, as well as the plot's amoral conclusion.
Gosford Park - Chiefly for the labyrinthine plot, a modern version of 'Upstairs - Downstairs' meets a classic Agatha Christie manor house mystery. Splendid are (in no particular order) Fry, Mirren, Gambon and several others.
No Country for Old Men - I'm not sure about the label 'masterwork', but to me it's truly impressing and has considerable impact.
Notes on a Scandal - Almost prefer Blanchett over Dench in this one.
Almost. As it is, it's a draw for me. Fine film!
Der Baader Meinhof Komplex - Probably not very interesting for most here, but quite an important film in my homecountry. I remember most of the incidents from my own childhood, was even stopped frequently in road blocks in the 80's.
The Lives of Others - Only twenty years ago, a third of my homecountry lay behind the iron curtain. If you want to get an idea what it was like living under the constant scrutiny of a KGB-like secret police and security service,
this is the film to watch. Brilliant Ulrich Mühe, went before his time.
Ratatouille - Wonderfully absurd idea. And I cannot help but love Remy.
28 Days Later - For having the good luck of hitting at just the right moment, reviving the 'classic' zombie genre at the time of the *SARS scare. (* for younger members: SARS was the fashionable thing to get the vapours before H1N1 gave us a new and even scarier hysteria)
Infernal Affairs and
The Departed - Basically the same ingenious plot, realised in two quite distinctive ways. American version is not a mindless remake, but a clever interpretation with a 'moralistic' end. In a
way. For a given value of
moral. I like both versions a lot. Also interesting is the prequel 'Infernal Affairs II'. I've yet to see the third part.
30 Days of Night - Initially, I didn't really like it. But the idea of vampires using the polar night has
some appeal. Also the eerie atmosphere of the landscape. Lots of splatter of course, comes with the genre, as the romantic teenie vampire flicks were still to be discovered.
Night Watch - Russian fantasy horror flick of 2004. Every bit as creepy and splatter as anything Hollywood comes up with, but with a considerable dose of unconventional Russian settings.
Blueberry - Mainly because of the visual experience. A hero of my youth finally found his way to the big screen. But the film version is entirely different, hardly sharing more than the name. Yet a distinctive streak of Moebius can be found IMO.
Corpse Bride - I can't help it, I have a thing for Burton's films. Also likely to be amongst my favourites is
Sweeney Todd.
Waltz with Bashir - Perhaps the most important and most
revealing film you're ever going to see about the war in this region. Although the plot deals with the Lebanon of 1982, it's highly topical today.
Layer Cake - I'm unsure how much impact this film really had on the 2000's, apart from Craig who was certainly not hired for Bond solely on this evidence of his ability. Anyway, it's had considerable impact on
me, which is all that is necessary to find its way onto this list. A great dirty little gangster flick, ingenious and cunning.
Identity - For a great idea and a terrific execution, keeping the surprises coming nearly every scene.
EDIT:
Oh, and of course
Donnie Darko - It's not because it's a perfect film. But it offers itself to so many different interpretations and theories that it can mean any number of things for any number of viewers. Conceptionally avoiding the definite explanation, this film and its characters open a whole range of different meanings, always keeping a secret in its tale.
I thought the Director's Cut edition of Watchmen was THE movie of 2009. I have seen it three times in total, which is very unusual for me for such a short period of time. 
