My vote goes to either Vagrant Story or Parasite Eve, both by SquareSoft. Both games are pretty short and I could see their stories being adapted into a 2 hour film without having to change all that much. Yeah I know Parasite Eve was originally a book and that book had a movie adaption, but I'm talking about the game's story here.
A Deus Ex movie done right would blow people's minds.
Or System Shock 2, specifically during the downfall of the Van Buren.