All The Myriad Ways: The way the Justice League and humanity are destroyed in the first chapter. Turns out it's All Just a Dream implanted in the minds of the villains to further Brainiac's master plan.
Civilian Villain: The entire Legion of Doom pretends to reform in order to discredit the superheroes.
Crazy-Prepared: Flash snatches Captain Cold's freeze gun away at super speed, only to find out it's a fake, allowing Captain Cold to whip out his real one.
Cut Lex Luthor a Check: The supposed motive for the fake villain reforms. They assert that the superheroes never actually make the world any better, they just maintain the status quo. Such technological marvels as Captain Cold creating oases in the desert and Scarecrow using his medical knowledge to cure the blind would be genuine examples of this trope if they were sincere.
Exactly What I Aimed At: When mind-controlled Supergirl is holding several heroes hostage, Green Arrow fires a glowing green arrow at her. She side-steps, then mocks him, saying he's out of kryptonite. Arrow retorts, "Who said it was kryptonite?" Cue John Stewart retrieving his ring from the arrow, then knocking her out.
Garden of Evil: Poison Ivy turns the Batcave into one when she attacks and brainwashes Batman.
Hurl It into the Sun: Captain Marvel throws Superman into the sun to burn out the mind control probes that were infecting him.
Identity Impersonator:In the final battle sequence, Parasite tries to use Kryptonite against the superhero wearing a metal suit with a giant S symbol on it. Turns out the superhero inside is Captain Marvel.
Mind Control: Brainiac's microscopic worms infect several of the heroes over the course of the story.
Mind Rape: Gorilla Grodd is able to make Martian Manhunter think that he's on fire through psychic manipulation, all the while when J'onn is actually at the bottom of the ocean.
Mythology Gag: The chief one is The Joker's outrage over not being included with the Legion of Doom. In the original animated series, the Joker was supposed to be a part of the Legion of Doom, but thanks to Executive Meddling, it never happened.
References to Lois Lane's interview with Superman in the first Superman movie.
Toyman (Winslow Schott) build a giant robot resembling the Jack Nimball Toyman.
One of Brainiac's experiments, a white monkey with a computer brain attached to its head, resembles Koko, Brainiac's pet "space monkey" from the pre-Crisis Superman comics.
Ray Palmer wears a suit that resembles the Gardner Gayle Atomic Knight.
Hawkman and Hawkwoman's suits resemble the Thanagarian deities from Legend of the Hawkman.
You can see the originalBatman costume in the Batcave. The one from before Bill Finger.
Not So Different: Batman has an epiphany that Superman's methods are somewhat compatible with his "Fight Evil Through Fear" philosophy. The crime rate in Metropolis dropped dramatically ever since Superman revealed his powers, most importantly X-Ray vision and super hearing, in an interview. Batman concludes that this news has left the criminals too scared to try anything, since Supes would immediately find them. He then congratulates Supes on using Fear to its fullest potential, but his reasoning only leaves Superman confused.
Subverted with Black Manta. Aquaman calls him out on his claims that his motive is revenge for the black people's slavery and discrimination by pointing out that Manta is using mind-control to enslave his minions (all black) into serving him. Manta comments on the irony, then says he doesn't care and keeps attacking.
Older Alter Ego: Several times in the story, it's apparent that Captain Marvel is really a 10-year-old boy.
Superhero Speciation: The old Elongated Man/Plastic Man feud about who should be the "stretchy guy" on the team. Plastic Man responds that since Captain Marvel and Superman are both flying bricks, and there's room for both of them, there can be two stretchy guys on the League.
Superpower Meltdown: At the beginning of the story, Flash is stuck running around the world at light-speed, and can't slow down. He's running so fast, he's racing himself.
Take That: Some fans have speculated that the miniseries was either Alex Ross doing a Take That or at least a "measured response" to the Identity Crisis miniseries.
This Looks Like a Job for Aquaman: While being tortured by Brainiac, Aquaman is able to contact the sea creatures to make a gigantic X pointing to his location large enough to be seen from the Justice League satellite.
Victory by Endurance: In the final battle, Hal Jordan faces Sinestro. Eventually, Hal reveals that he's not using his own ring, but Sinestro's spare ring, with a chunk of blue kryptonite on it to make it look green (yellow + blue= green). Hal could either defeat Sinestro normally, or wait until both rings were depleted (they drew on the same power battery). Option 2 happens, and Hal defeats Sinestro with his fists.
Wolverine Publicity: On the cover for the second trade paperback of the series, the Joker is featured prominently standing among the Legion of Doom members. He is far from the main villain, is never considered to be a member of the Legion, and really only makes cameo appearances in the story itself. To be fair though, a lot of the characters on the covers parallel characters on other covers, and Batman is the one who's smack dab in the middle of the first cover...