My initial take is that it (like the 90's in general) were pretty abysmal, but you'll need to stretch your mind back all the way to 2000. It was a strong decade for Pixar (Nemo, Monster's Inc., The Incredibles, Ratatouille).
As mentioned in the general movie thread, Wes Anderson's Fantastic Mr. Fox was exceptional, but I'd also nominate his Life Aquatic (which I know doesn't appeal to everyone here.)
The best science fiction film for me was Children of Men followed by Inception (the former being considerably better). Can district 9 get honorable mention for basically being an 80's sci fi flick?
Miyazaki's output for this decade did not feel as strong (jesus, the guy is single-handedly keeping 2D animation alive), though Spirited Away, Howl's Moving Castle and Ponyo are still all very good films (I think most would argue that Castle is the weakest).
Bringing Nolan back up (just to cause grief for Skykid), I do think Dark Knight deserves mention; though I also don't think it is competing with much. One of the darker, grittier films of the decade.
As far as horror, the two films from this decade I found much interest in were both British: 28 Days Later and The Descent.
I hate comedies, though really enjoyed Tropic Thunder. Should I mention Black Dynamite...hmmm. I'll leave you guys to fill in this catagory, as I will with romantic comedies.
I know you're all gonna list Lord of the Rings as well, but this decade was the end of my appreciation for Peter Jackson's talents.
So guys, time to put on your thinking caps. I've got to be missing dozens of films since I don't go out to the theatre so much, and my netflixs cue is just filled with Dr. Who episodes

Can we actually make a list? Top 25 films? Let the heated debates commence!