Cerebus - It would have to be an animated anthology of some kind, as a movie version would be pretty much impossible. Also, they could stop after the first four books.
Fables - Another that would work as an animated anthology.
Robocop vs Terminator - I'd be happy if this came out like some of the other DC/Marvel DVD animated movies.
Aliens vs Predator - the original miniseries set on the desert planet.
Lobo - Specifically the Paramilitary Christmas Special. That would be an awesome 30 minute show.
Howard the Duck for President - The comic book was an unabashed champion of 70s era liberal politics, and the Presidential campaign story arc might just be it's highest point.
Blacksad - While the first book remains the best, all three Blacksad books would make for awesome film nior movies.