- A few seconds into the first cutscene, Commissioner Gordon notes "it's always sunny in Metropolis"
- After being saved from some cops by Joker, Scarecrow exclaims "Don't you just love it when a rescue mission comes together?"
- A rather surprising one from a bystander in Smallville."Whenever I see that big water tower in the middle of town, I like to imagine that it serves as the comfortable home for a family of orphaned cartoon characters."
- Might have been Foreshadowing, since the show's reboot was in development at the time.
- A Gotham bystander might be heard to say "I can't believe Bryce prefers Lex Luthor's card to mine."
- While fighting Poison Ivy's henchmen during Count Vertigo's quest, he says "One Ivy Goon! Two Ivy Goons! Ah, ah ah!"
- There's a cafe in the Gotham City Museum in the level "Fight at the Museum" run by The Coffee Chain.
- One of the hints for the bow tie challenge reads, "Being cool isn't hard when you've got a library card."
- One of the Scarecrow's lines if he's unable to solve a puzzle is warning anyone else against joking about him not having a brain to work it out.
- Flash doing the floss and Cyborg doing the dab is shown when the Justice League escape from Darkseid.
- When Grodd shows up during the final battle against Darkseid, Harley Quinn suggests that he throw a barrel at him.
- Doubles as a Mythology Gag, considering the developers, but during Mongul's sidequest, one of the potential players mentions that the "Golden Fury" racing spinoff is called "Golden Fury R".
- When Mallah and the Brain pick up a collectible, they will mention that they intend to use to take over the world, before asking if that was the goal of another Brain.
- Ares is found pondering how "War always changes."
- After completing Ares' quest, he texts the player that his idea for a conflict-inducing movie would be called "It Came From Krypton".
- In a sidequest, a darkness-obsessed villain tasks the player with disabling the Gotham City lighthouse. He later texts them that he's come up with a new plan - to block out the sun using a giant satellite dish.
- After helping a couple of Poison Ivy's plant-themed goons to hijack the Daily Planet's printing press, a defeated Jimmy Olsen suggests they "make like a tree and get out of here".
- During the boss fight for the Gorilla City level, a random miniature Statue of Liberty is tossed into the arena.
- One Apokolips Gold Brick involving a Man-Eating Plant has a nearby guy tell you to "Attack Its Weak Point for massive damage" to get the brick out of its maw. Said plant is also named Seymour
- Befitting his name, the pre-quest quote for Scarface (and The Ventriloquist) has him stating "Say hello to my little friend!"
- During Scarface's quest, one of the goons holding his repair items says "Do I look funny? Do i amuse you?"
- One Minikit in "Apokolips, Wow!" involves having a Lantern-pad-created hand scoop it out of some molten lava, after which it gives a thumbs-up while sinking back in.
- Do Copperhead's mission in the Swamp, and he'll mention snakes, stealth missions, and cardboard boxes.
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