Apocalypto. I actually consider Pan's Labyrinth 2007 since that's when it expanded, even if I put in 2006 Apocalypto was still better though.
The Descent and SAW III (which despite all the smug eye-rolling and face-palming reactions it typically gets is full of interesting themes, emotion, and character arcs) were better than everything else that year.
The Departed was a rather bland, generic crime drama, and The Prestige was pretty bad. Couldn't have cared less about the characters and the execution of the story was self defeating toward its intended message.