Both of Christopher Nolan's first two Batman movies were inspired/loosely based on Batman graphic novels.
Batman Begins = Year One, The Killing Joke
The Dark Knight = The Long Halloween
The latest rumors, as reported by Entertainment Weekly, Ain't It Cool News and Slash Film, is that Nolan's last Batman film, 'The Dark Knight Rises' (Batman 3), is inspired by Batman: Prey (1990-1991).
A full plot breakdown of the graphic novel can be found at the wikipedia page (Batman: Prey). While the original print graphic novel can be bought on Amazon.com for $400-600.
"This rumor, however, is one we’ve been hearing for a while. In November, we ran a story speculating that Tom Hardy (Inception) would be playing Dr. Hugo Strange, “a genius, mad scientist who becomes obsessed with Batman, learns his secret identity and ends up dressing up like him,” in Christopher Nolan’s The Dark Knight Rises. One of Strange’s most famous roles is in the Batman: Prey storyline, written by Doug Moench and drawn by Paul Gulacy and Terry Austin from late 1990 to early 1991. It begins with a task force, headed by Commissioner Gordon, assigned to hunt Batman and devolves into Dr. Strange dressing up as, and psychologically toying with, Batman and Bruce Wayne once he figures out his identity. Interesting. Doesn’t Batman become a fugitive to be “hunted” at the end of The Dark Knight?"