The film, starring Christian Bale, came out on top at the ceremony in Burbank, California, on Wednesday night, which is hosted by the Academy of Science Fiction, Fantasy & Horror Films.
The Dark Knight was named Best Action-Adventure Thriller, while late star Heath Ledger was honored posthumously as Best Supporting Actor. The sequel also took prizes for its script, special effects and score.
Angelina Jolie took the Best Actress trophy for Changeling and her partner Brad Pitt's movie, The Curious Case of Benjamin Button, landed three awards -- seeing off competition from Twilight to be named Best Fantasy Film.
The picture also garnered a Best Supporting Actress honor for Tilda Swinton and a prize for its makeup effects.
Will Smith's son, Jaden Christopher Smith, was honored with the Best Performance by a Younger Actor award for his turn in The Day the Earth Stood Still, Swedish vampire horror Let the Right One In scored Best International Film, and Wall-E was Best Animated Film.
In the TV awards, mystery drama Lost was named Best TV show and Battlestar Galactica landed the Best Syndicated/Cable Television Series honor, as well as acting prizes for stars Edward James Olmos and Mary McDonnell.
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