I think we're on to something with Ghost in the Shell. Not only does this film have the same problems that the Matrix had that made it so susceptible to being riffed (Taking itself too seriously, lots of techno mumbo jumbo), but there are a lot of scenes that are slow and dull that can provide lots of riffing time.
I would LOVE to see them riff it's sequal, innocence. That film is so bad I don't even label it as a film because nothing happens in it.
And besides, wouldn't it be awsome to have cover artwork that featured Mike and his gang in anime form?
And these titles aren't hard to find either. Manga just released an anniversary edition, and Dreamworks still has Innocence on their list.