I have thought about how in Indiana Jones and the Kingdom of the Crystal Skull, the Soviet Union officials are the villains, but they are shown to be acting in reaction to existing United States weaponry and technology that is threatening their country and government. RedLetterMedia does good job of explaining this in their review of the movie.
However, their main goal is to use the titular skull for mind control against Earth's population.
I always sorta rooted for Raoul Silva in Skyfall. Dude blows up the MI6 building and kills M? Critical support to the man and his struggle against the British secret intelligence.
Other than that I don't really remember that movie but I remember sort of rooting for him when I watched it a long time ago.