Ho Yay: Probably unintentional, but there's a brief moment where hunky, square-jawed Captain Wilson gives Stryker a meaningful look and then turns and walks away, almost as if he means for Stryker to join him somewhere more private. Stryker waits a moment and then follows him.
"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.
Fanfic Fuel: All those alternate realities the characters visited (not counting ones already previously shown, like The Dark Knight Returns), including one where Alpha Centurion is the hero of Metropolis and one where Barbara Gordon remains as Batgirl after her father was shot by the Joker instead.
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, the Bruce of the mainstream DCU's disgusted reaction mirrored that of many fans to both 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. Other tie-ins are additionally freaky, such as as the Robin and Catwoman ones, where everything fades to white instantly almost without explanation, and in Selina's case, happened so suddenly that she didn't even have time to react.
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 versions, the shock and disgust of the mainline Bruce).
The deaths of the various members of the JSA as Extant ages them to their proper ages, killing several of them in the process.
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.
Similar to the above example, one of the time anomalies sends Superman to Krypton, where he gets to meet his birth parents...only to be forced to watch the planet explode before he can do anything to try and save them.
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.)