As seen in the DS version, there's a comedic What the Hell, Hero? moment when Robin laughs at two policemen frozen by Mr. Freeze.Batman's expression is priceless.
Batman using the Batcomputer to shop at "www.awesome-capes.com". Even better, it's an actual promotional site for the game.
When the villains are playing poker, Killer Moth keeps getting distracted by the lamp near him.
In one cutscene, Batman and Robin notice the Bat-Signal in the air. Batman tries to keep Robin from leaping off the top of the building, but Robin does so anyway and (presumably) eats pavement. Batman shrugs his shoulders then starts going down the fire escape.
Batman defeats Catwoman by leaving a saucer of milk out for her, then arresting her while she's drinking it like a cat.
Clayface makes himself a house out of gold bars while he and the Riddler rob a bank.
Bane takes himself out by throwing a police car into the air to intimidate the GCPD. The car lands on his head, leaving the police to tow him behind them to get him back to prison. He's so heavy they're barely able to do so.
The game has a field day with the ridiculousness of Killer Moth's name and design, with reporter Vicki Vale's reaction to him being "seriously?" and the fight against him. He is flying around a giant light bulb and to fight him on the ground you have to turn it off. His quote is "The light! The light!"
The cutscene when they arrive at LexCorp:
Superman: I'm Superman. He's Batman. Receptionist: Uh huh. Are those last names? Superman:(Beat) Uh, one name each. Batman: Like Madonna.
Lex Luthor is described by Vicki Vale as "some bald guy from Metropolis."
The news crawls at the beginning of each cutscene usually have at least one.
In the opening to the Arkham Asylum mission, news reporter Vicki Vale asks how smart it really is to put all of Batman's costumed villains together in one spot, before noting that it's at least better than the mayor's plan of letting them all duke it out in a walled-off area in the city. "Now that would never have ended well."
Some characters have guns, some have swords, some have other cool weapons, and Black Manta, despite having a suit full of weapons, slaps his opponents with a fish.
Joker: Oh, hey Lex! You've come to get your watch back, or did a bus to Metropolis get lost and break down? Lex:First, I don't take the bus. [a helicopter comes up] Lex: Second... Yes, give me my watch.
The entire elevator sequence when Batman and Superman visit Lex Luthor. Among other things, Superman checks on a game's score for a janitor with the help of his super-hearing.
Ra's al Ghul's pre-unlock fight combines this with a delicious Shout-Out.
Joker singing "I got the whole world in my pants". Batman and Lex Luthor simultaneously tell him to shut up. Right before the cutscene ends, he shouts "Pants!"
The second level has Batman get brainwashed by Brainiac resulting in Robin and Alfred spending the level trying to break the mind control. The fact that you play as Alfred in this level means you have the option to make Alfred beat the crap out of Batman.
When Batman takes off to go into space, he fries some ducks by accident. Those who weren't fried fly away with him.
Some of the banter during gameplay is pretty amusing, such as Alfred wondering if Batman is going on a rampage because he used the Batmobile for grocery shopping, or Robin saying he heard that Batman Can Breathe in Space.
When the heroes/villains damage Braniac's ship enough, everything starts going out of control, and the Lanterns under Braniac's control start firing off energy pulses. Multiple heroes/villains get hit by these pulses, causing the emotion corresponding to whatever color they were hit by to be amplified. Which leads to them acting very...different from how they normally act. Whaddaya mean, O.O.C. Is Serious Business?
Since they weren't affected, this causes Batman, Robin, Green Lantern, Cheetah, and Martian Manhunter to be the straight men for a large portion of the game.
In particular, Flash, who was hit by orange light (Greed), gets a lot of hilarious moments where he tries to snatch up everything around him, from traffic lights to chickens.
His greediness also leads to him constantly saying that he wants everything he sees and declaring it to be his.
Straight after Green Lantern's mysterious disappearance, this scene follows:
Robin: Where'd they go? Is Green Lantern...dead? Wonder Woman: That explosion killed him?! Batman: We don't know if he's dead. Joker: That would be a shame. He's so handsome and sweet! Cyborg: I'm really afraid that might happen to us! Grundy: [hugs Joker and Luthor] C'mon, guys! We'll make it! No problem! Luthor: I hope so! Robin: What the heck is going on?!
Joker, even when he's amplified by love, is still the Joker as when he tries to take control of Brainiac's ship, it goes out of control.
Larfleeze's boss fight. Aside from constantly screaming "MINE!" throughout the game, he's also tricked into accepting a construct of Hal Jordan when he wanted the real deal.
Booster Gold's idle animation is taking a selfie of himself and Skeets. The photo he takes is shown to Skeets afterward.
When Lex Luthor is disguised as Hawkman, and walking through the crowd in front of the Hall of Justice, there are several stands selling superhero merchandise. Superman's is completely crowded, but the only person at Aquaman's stand is a bored clerk, with not a single customer, and loads of merchandise.
Batman's Joker impression is hilarious, but not as hilarious as Robin's bizarre decision to give Lex Luthor a Southern drawl.
As expected, Superman and Clark Kent turn into each other. However, since the game doesn't take itself seriously at all, it's pretty hilarious in practice. By that, we mean a phone booth drops down out of nowhere, Clark dashes in and emerges as Superman, and the phone booth promptly falls to pieces behind the proudly grinning Man of Steel.
Green Loontern (Daffy Duck as a Green Lantern) in general.
When fighting Brainiac in London, Superman shouts, "Don't do it! The people!" which is a particularly Narmy line taken straight from Superman IV: The Quest for Peace.
The entire end credits sequence, playing a loop of the '60s Batman series theme with Batman (voiced by Adam West) and Robin climbing the side of a building and bantering with various characters.
How do you defeat the Joker in the '60s level? By building a jukebox and doing the Batusi.
The ending of "The Squad" DLC. It turns out that all this chaos was caused by Killer Moth, who was too technologically incompetent to hack in and thus tried breaking in. Amanda Waller just sounds exasperated, and the Squad promptly give him a beating.
One of the trailers is just Batman attempting to brood. Attempt is the keyword here.
Batman: Here, at the edge of the universe, I look into the abyss and— Superman: Batman! Batman: I look into the abyss— Superman: Bruuuuce! Batman: Seriously? Superman: Is that a new spacesuit? [beat] Superman: Your suit looks really good, is all I'm saying! One hero to another, it's really working for ya. [beat] Superman: Right! Brooding. Carry on!
60s Batman has the same invisibility power as other stealth characters, but he doesn't turn invisible. Instead, he just holds his cape up and sneaks around in plain sight.
Similarly, Cyborg's stealth mode is him turning into a laundry machine.
Saint Walker being completely useless in the opening battle, only capable of repeatedly stating that he's completely useless without Hal (or another Green Lantern) around and hoping that he'll show up.
The Superman IIITilting Tower of Pisa scene was referenced in "Europe Against It", with Superman straightening the Tower, only for Brainiac to just knock it back to it's original position
for the game.