3. JLA: Tower of Babel (Mark Waid)
Tower of Babel is probably one of my favourite Justice League stories, simply as a result of its thorough deconstruction of one of the very traits that makes Batman such a powerful hero: his paranoia. In Tower of Babel, it's detailed that Batman has been compiling data on his fellow league members, collating secret identities and weaknesses just in case
any of them should ever go rogue (a smart move if you ask me, Superheroes go rogue
all the time). However, when Ra's al Ghul manages to gain access to these files, it's brown trousers time for the League, who find themselves for the first time completely and utterly exposed to defeat. This story had a knock-on effect in main-canon Justice League and saw many of its members turn their back on the Dark Knight for his betrayal of trust, even though his actions were of course taken with the safety of the planet in mind. For me, this'd be a perfect way to establish the League, as well as their various weaknesses, and also set up further JLA movies in which Bats must re-earn the trust of his super-colleagues.