Most of the comic book influences on Batman Begins are fairly evident. Everyone points to Frank Miller’s Year One, the redefining four-part series that put the “Dark” back in Dark Knight, and they’re right to hold that book up as the major influence. Begins relies heavily on Year One for a number of things, not least among them the exploration of the Bruce Wayne/Jim Gordon relationship, the exploration of the Bruce Wayne/Alfred relationship, the Gotham Monorail, the mention of the Joker at the end, the entire character of Flass, the entire sequence where Batman calls a squadron of bats to his aid (a bat-talion, am I right? Guys?) and, of course, the entire bat-flies-through-window genesis of the hero himself.
So Year One is the obvious one. Nolan and David Goyer pilfered little things from other famous Bat-books as well, often just an image or a line of dialogue. Here’s the Scarecrow in Loeb and Sale’s The Long Halloween, another popular arc:
Goyer brought this to Nolan and said “I think Katie Holmes and the little kid who will eventually grow up to be Joffrey from Game of Thrones would look really good if we added them in front of the horse here” (paraphrased) and Nolan said “true dat, brah” (not paraphrased) and ran with it:
The red eyes and flames are an admittedly nice touch.