BioShock effectively toyed with players' perceptions of free will, all within the confines of a linear narrative. In this spoiler-inducing piece (warning!), Gamasutra looks at how the game gave players a feeling of control without actually handing it over.
In linear games, there's always the lurking danger that players will think they've got a shred of influence on how the game unfolds. In an effort to resolve this, many games employ a narrative voice to let players know what exactly what they're supposed to do and give them at least a bit of motivation for doing. Despite how commonly it's used, this device has a tendency to backfire when the commanding officer/mysterious stranger/computer geek is annoying or patronizing.
So it's nice to see BioShock not only manage to make this narrator and guide an interesting character, but also critique the entire relationship between this figure and the protagonist and player.