I have a game I've been fantasizing about and I think I could make it work. It has to be a game, not a story, because I want to pull a kind of trick on the player. It's not that unusual in fiction for a character to start out on the side of the "bad guys", have a realization that his side is the one that's bad, and then go on to save the day. (James Cameron's Avatar is a recent example.) I want to start the player out on the side of bad guys that appear good, as in Eliezer's short story "The Sword of Good", and then give the player the opportunity to fail to realize that he's on the wrong side. There would be two main story branches: a default one, and one that the player can only get to by going "off-script", as it were, and not going along with what it seems like you have to do to continue the story. (At the end of the default path, the player would be shown a montage of the times he had the chance to do the right thing, but chose not to.)
The actual story would be something like the anti-Avatar; a technological civilization is encroaching on a region inhabited by magic-using, nature-spirit-worshiping nomads. The nature spirits are EVIL (think: "nature, red in tooth and claw") and resort to more and more drastic measures to try to hold back the technological civilization, in which people's lives are actually much better.
Does this sound appealing?
As an example of a flash game with similar story branches (albeit a pretty different plot), there's endeavor.
If it's worth saying, but not worth its own post (even in Discussion), then it goes here.