While most of the film material is completely original, the plotline of Batman developing countermeasures against his Justice League teammates as a deterrent, only to have the plans stolen and used against the Justice League is based off the 2000 JLA storyline "Tower of Babel".
In the original comic book storyline it was Kyle Rayner and not Hal Jordan who was serving in the Justice League as Green Lantern since this took place after Hal Jordan had become Paralax and then Spectre prior to this storyline's release and he wouldn't serve as Green Lantern again until the Green Lantern: Rebirth storyline that was released five years later.
In the original comic book storyline Wally West was serving as the Flash instead of Barry Allen. This was due to Barry Allen being lost in the Speed Force at the time and he did not officially return until 2008, which was 23 years after he was originally killed off.
For the Justice League members that appeared in both the original comic storyline and the film, the contingency plans that Batman developed differ between each version. A few examples from the comics are that Superman was exposed to a special red kryptonite that caused his skin to turn red as a result of absorbing too much yellow solar radiation or that Green Lantern's ring caused him to go blind due to a post-hypnotic suggestion that made him believe he was blind which was placed while he was sleeping. In the film Superman was shot with a Kryptonite bullet, and Green Lantern was made to doubt the powers of his ring by giving into fear.
A slight difference between the lineup in the Justice League between the original comic book storyline and the film is that Cyborg was serving in the Justice League in the film, while in the comics both Aquaman and Plastic Man were part of the Justice League.