Cavalary: - The truth about the "terrorists" in Deus Ex. Also talking to the AI at the end. (Not necessarily great in themselves, but as part of that game, which is great overall.)
EDIT: Added that PS:T piece I was referring to.
The Deus Ex AI part where it tells you that God is the dream of perfect government?
Yeah, I loved that part - I've banged on it about it many a time on here, mainly when defending the plot from the haters
What else? Many parts of Outcast, struglling to remember the specifics though, its been a while, too long!