Baldurs Gate, start to Throne of Bhaal, has the best story in a game I?ve ever experienced, mainly due to the characters and how they all act and react differently to the story. KOTOR II is beautifully written, the cryptic messages hidden in dialogue make the game bloody astounding once you understand it and can see pasted the thin veil of manipulated truth and lie.
What can I say? I love finding out I?ve been used as a puppet in games, and/or betrayed. Adds a whole new level to getting even with the basteds. Worked in Deus Ex for sure.