From a purely technological standpoint, I have to say Avatar was the best movie of 2009, and I'd doubt that anyone could argue that successfully. I saw it in IMAX 3-D, and quite honestly between the spectacular 3-D and the completely fantastic CGI that went into the making of the movie, it was beyond a doubt the best thing to come out this last year. That is, purely on a technologicial/effects level. On a story level, was it really that different from Dances with Wolves, with a pro-green message bludgeoned in?
On other levels I'd have to rate District 9 as the best movie of the year. Firstly on a financial/"how the fuck did they manage to make it" level, it easily qualifies. It was made largely outside traditional Hollywood channels, on essentially a shoestring budget. The slum/reserve/whatever that the aliens were restricted to wasn't built for the movie. When the movie started filming, the SA government was still moving actual humans out of that 'city' who had lived there for I don't know how long. Sure, it was heavy-handed with message, but the more you learn about what went on behind the scenes, the more in awe you become of the final result.
Star Trek.... a bubblegum flick. Ok, the fan in me admits that the 'bible' of the Trek universe had gotten far too unweildy, and needed to be thrown out the window to start from scratch again. The movie viewer in me however, has just three words: Lens fucking flare. If I never see a lens flare on a giant screen again, I will be only too happy. And moi, clearly you don't hang around with the same kind of Trekkies I do.
UP and Cloudy With a Chance of Meatballs. Two different films from the current leaders in CGI-movies. Both were great, the storylines were entertaining, and it's continually amazing how far the field has come in such a short time. Bravo to both companies.
Sadly, I'm afraid most of my movie-viewing tends to fall within the realm of SF, so I can't comment too much upon movies which fall outside that genre. Sherlock Holmes was quite well done, RDJ is absolutely at his peak right now. I may one day watch The Blind Side, because so many people are saying such good things about it. About the only movie outside the "SF ghetto" that I'd really like to see right now though, is The Wrestler.
Personally, I'd like to say Watchmen was one of the best films... but sadly I can't. It was a strange beast. The movie stuck too close to the comic to really be accessible to the general public, yet diverged too much from the same source for the die-hard fans to accept it. I truely believe it was the best possible adaptation that could have been brought to the screen, and am willing to accept the changes that were made, but that seems to put me in a minority. (Even if you added another two hours, I don't think audiences would have been ready for a giant space octopus.) Strangely enough, the strongest memory I have of the movie is watching it on IMAX opening night. Despite the 'R' rating, and huge warnings, two families brought their kids. They had no problems exposing their children to the death, violence and gore that fills that movie, yet one family walked out at the rape scene, and the other walked out during the sex scene. Still bothers me that they considered it ok to show their kids people being graphically disintigrated or burned alive, yet god forbid their kid see anything to do with sex....