"Seinfeld" Is Unfunny: Or, rather, Zero Hour!is funny; it has been noted that, what with Airplane! and all, it's very nearly impossible to watch Zero Hour! with a straight face anymore. It's also not as overly melodramatic (and therefore not as silly) as some other Disaster Movies might be, but it gets lumped right in with them anyway. Case in point: Warner Home Video marketed the DVD as part of their "Cult Camp Classic" line of films.
The Batgirl of her timeline reveals she and Bruce are romantically involved, and when she attempts to kiss him Batman recoils back in shock. Batman Beyond made them lovers as part of their backstory and Batman: The Killing Jokesees the two end up having a sex scene, both to massive outrage. To make it worse, mainstream!Bruce's disgusted reaction mirrored that of fans' reaction to the animated versions.
Batman is sent to a timeline where he was shot by the mugger instead of his parents. Flashpoint would provide us with a similar reality, only it ended up even worse for Thomas and Martha.
At one point when Superman and the Batmen are guarding a rock concert, the Golden Age Batman expresses disgust towards rock music, long before Atop the Fourth Wall turned Batman hating rock into a meme.
Kyle: Yeah, well... probably bound to happen sooner or later, anyway.
As noted on the main page, this was meant to fix the remaining problems Infinite Earths had brought up, but it ended up introducing more problems which led to Infinite Crisis being used to fix those issues.
Nightmare Fuel: The time-erasing void consumes entire universes, and the effects are represented as everything in the comic fading to white, including panel borders, until nothing is left but blank pages. The Action Comics tie-in is especially scary, as Lois Lane fades midsentence and has to watch everything die around her.
Older Than They Think: The much-derided idea of Bruce and Barbara as lovers from Batman Beyond and the adaptation of Batman: The Killing Joke? Actually happened here first, as the alternate Batgirl seen throughout the story, introduced in Batman (Vol. 1) #511, was in a romantic relationship with her Bruce (much to, mirroring fan reaction from the animated version, the shock and disgust of mainline Bruce).
One of the time anomalies sends Batman to the night his parents were murdered, except in this reality he was shot and killed instead of them. After spending all night fruitlessly searching for the killer, he decides to return to Wayne Manor, and hopes that meeting each other can help with their respective losses... only to learn the anomaly has gone and the Waynes have vanished as if they'd never existed. Damn.
Critical Research Failure: The old clockmaker mentions three apostles by name: Peter, Bartholomew, and... Luke? (A double failure because two other named gospels, Matthew and John, would have been correct choices.)