Some notes I've taken on both Batman Begins and The Dark Knight:
Aside from the obvious inspiration from Year One, there are also a lot of other stories that have impacted the films. Scarecrow and Ra's al Ghul are clearly based on Batman's first two supervillains, Doctor Death and the Monk. Doctor Death and the Monk both predate the Joker and Catwoman, as they first appeared in Detective Comics before Batman even got his own self-titled series. Doctor Death debuted in Batman's third appearance, and the Monk debuted in Batman's fifth appearance. Doctor Death was a scientist who developed a lethal chemical agent from pollen extract and tried to use the poison to extract money from wealthy Gotham citizens. He was assisted by a large East Indian manservant named Jabah. In an attempt to evade capture by Batman, Doctor Death ignited the chemicals in his lab, presumably killing himself and Jabah in the resulting explosion. In the next issue of Detective Comics, Doctor Death reappeared, with a new accomplice named Mikhail. The character was revived in a 2003 Batgirl story, his origin updated for an era of increased terrorism awareness. This modern version of Doctor Death is a producer of biological weapons, selling them on the black market to terrorists and other criminals. The Monk was the supernatural leader of a cult known as the Brotherhood. He was a vampire, hypnotizing Batman's first girlfriend, Julie Madison, and eventually turning Batman himself into a vampire. Both are sedated eventually. In Batman Begins, Ra's uses a lethal chemical agent developed from a rare blue flower in the mountains. He is the leader of a cult known as the League of Shadows, and planned to use the chemical agent to destroy Gotham. He had an East Asian decoy. During training, Bruce ignited the chemicals in Ra's fortress, presumably killing Ra's, the Ra's decoy, and the rest of the cult in the resulting explosion. Scarecrow developed the chemical agent, and used it for the purpose of psychological experimentation. He was also somewhat involved in messing with the economy like Doctor Death, because when he affiliated himself with Ra's, he was under the impression that Ra's was going to hold Gotham for ransom (this is explained by Ra's during the final fight with Batman). Scarecrow also used the hallucinogen to mind-rape Batman's first girlfriend, Rachel Dawes, and later Batman himself. Both are sedated eventually. Ra's later reappears, with a new decoy and following. He is revealed to be a producer of biological weapons, which he sells on the black market to other criminals (Scarecrow can't develop the toxins without the flower). Doctor Death and the Monk were around during Batman's third and fourth appearances, around 1939, so it's like Goyer wrote Year One elements like Carmine Falcone and the mob into the films (according to Year One, Carmine Falcone would be one of Batman's first "normal" villains chronologically), and then wrote his first two supervillains into the film (except using more .... interesting characters to fill the roles). Like, Goyer placed Year One villains in front of Batman villain's first historical appearances in the '30s and '40s, so it almost follows the comics; he's suggesting Year One (mob) > Detective Comics #29, 31 (Doctor Death, the Monk) > Batman #1 (Joker). So maybe the next villain will be Catwoman?
Batman Begins also takes some inspiration from Year Two. Bruce's first girlfriend, Rachel Dawes, shares the first name of Rachel Caspian, Bruce's Year Two flame. Joe Chill's death from Year Two was adapted in some form for Batman Begins; Bruce plots to kill him, only to have someone beat him to it.
The Dark Knight uses story elements from both The Long Halloween and Dark Victory. Nolan has already cited these stories as influences, but I'm trying to gather specific details from them to see just how they influenced the film.
Some elements taken from The Long Halloween are Batman, Dent, and Gordon working together, the mob using the bank, the mob having to resort to hiring "freaks," the "I Believe in Harvey Dent" campaign slogan, the birth of Two-Face, and Two-Face targeting the people responsible for his disfigurement.
As for Dark Victory, the role of the Hangman Killer seems to have been taken, in part, by Two-Face. Hangman, otherwise known as Sofia Gigante Falcone, kills police officers who had ties to her father before his death. Two-Face targets public officials who were responsible for the death of his girlfriend. Interestingly, the district attorney who was appointed after Dent became Two-Face in The Long Halloween, Janice Porter, began having an affair with Dent in Dark Victory .... before she was slain by him. The Joker also seems to have taken part of Hangman's role; he kills public officials and leaves clues at the crime scenes as to who his next victim(s) are going to be. Two-Face is shot off a cliff towards the end of Dark Victory, and is pushed off a ledge towards the end of The Dark Knight; in Dark Victory, he is shown to have survived the fall, but in The Dark Knight, he is likely dead. Finally, the character of Anna Ramirez - the commentary on Batman: Gotham Knight indicates that she is based on Renee Montoya, which is probably true, but if you look closer, you'll see that her purpose in The Dark Knight is to fill the role of Laureen Wilcox from Dark Victory. Ramirez and Wilcox are both newcomers to the GCPD, and are generally good people aside from, y'know, being on the mob's payroll. Ramirez is involved in the planning of Harvey's "death." She is eventually confronted by Two-Face, but is spared by chance. However, she does get *****-slapped by Harvey's gun in the middle of the street. Wilcox is involved in planning the capture of Two-Face and bringing him to face trial. She is eventually killed by the Hangman Killer (who I've already said appears to have influenced the character of Two-Face in the film).
Finally, The Killing Joke. We've been told that this was one of the inspirations for the Joker in The Dark Knight. Aside from the Joker's "foggy memory" when telling his origin, there is also an extremely obscure, behind-the-scenes character in The Killing Joke named Colleen Reece, who is a friend of Barbara Gordon's. Colleen Reece? Coleman Reese? Coincidence? Alright, I got nothing.
