Um, I'm not sure if anyone has noticed this yet, or brought it up, but in Uncle Orsons' latest review of Everything, he talks about Aeon Flux being based on a video game. (http://www.hatrack.com/osc/reviews/everything/2005-12-04.shtml)
The recent live-action movie is acutally based on an animated series (with episodes of various lengths) by Peter Chung. It was originally was shown on MTV.