This exchange in one of the Riddler's Challenge room.
Hostage: Why doesn't he just tell you what he wants?
Batman: [flatly] ...Because he's INSANE.
Made even funnier by the fact that a few moments earlier, Riddler was talking about how he was NOT insane, since that implied either "mental illness or derangement, and [he] suffered from neither". Of course, Batman didn't have any of it.
Also, in one of the Riddler's interview tapes, Nigma receives a magnificent Take That from Strange, who is explaining the strategy he used to learn Batman's identity.
Riddler: I know you were lying, Strange. There's no way that you could have figured it out! It's some kind of trick. It must be!
Strange: Oh, I use no tricks, no childish puzzles. I simply created a psychological profile of the man most likely to be the Batman, and then matched it against the most logical candidate. I was right, of course.
Riddler: Well, who is he?!
Strange: Ah, but that would spoil the game for you, wouldn't it?
Riddler: You must tell me! I implore you Strange! I-
Strange: Really, Edward? If I could figure it out, it must be child's play for you.
Riddler: But I... I...
Strange: Interesting. Tell me Edward, how is the Riddler like a blank dictionary?
Catwoman: You're right. I think I chipped a nail back there.
That's funny enough, but much later in the game the lines are reversed between the two after Catwoman helps Batman. Batman delivers it pretty poorly, however, and Catwoman calls him on it.
When Batman confronts Penguin at the museum, Penguin accidentally (presumably) hits one of his own Mooks with his umbrella in the crotch.
Better yet, if you die in that room (and on harder difficulties, you probably will), you get to watch it over and over - and it gets funnier every time.
This line from the first Riddler Room:
Riddler:Well done, Dark Knight! You figured out how to open a door!
You can try to unlock the Riddler security boxes before they are activated, and the Riddler will tell you wait a little while. Try three times, and he'll finally get annoyed enough to tell you piss off until he's activated them.
When you first try to unlock them.
Riddler:(on the first try) You're getting ahead of yourself, Batman. Those contraptions are of little use to you... for now.
Riddler:(second try) Oh, Dark Knight, you are being impatient. I will reveal the purpose of those when I am good and ready!
Riddler:(third try) Are you really so stupid that you cannot even understand a simple instruction, Batman? Ugh, don't answer that. The childlike gibberish you are bound to spout will just be embarrassing. Let me explain one last time. Ignore those control boxes for now. They are not activated, as in they do not work. They will, but only when I am ready. Was that clear enough? Good...
Before you enter the Church after Riddler has taken over.
Riddler:(after the first try) I'm waiting for you in the church, Dark Knight, waiting to prove that I am better than you. Come and see me, if you dare...
Riddler:(second try) Oh come on, it won't work! A child could see that! You need to come to the church.
The first time you encounter Harley, she's cartwheeling and back-flipping down to you. She's actually trying to ATTACK YOU. If you counter her kick, you fling her to the side. If you don't? You get hit in the face, and it seems like you're about to have a fight with Harley...until you take her down in one punch anyway.
After she leaves, four of the mooks with her are pointing guns at Batman. The following exchange is priceless.
Mook 1: Just walk away, and everything will end okay.
Tragically, none of the four thugs in the following predator tutorial are designed to be taken out with an inverted takedown (which hangs them from the ceiling).
Not designed to be, no. But you can take one of them down this way if you swing to the third gargoyle on the left fast enough.
If you go to the Iceberg Lounge early, or attempt to enter the front door where Nora Fries is being kept, Batman can knock on the door and a mook will peek out. Grumpily asking what you want before realising who he's talking to.
This then gets an ironic reprisal when you go back to the Iceberg Lounge after Penguin is defeated. The undercover cop comes to the door angry and then apologizes when he sees it's Batman.
When Vicki Vale reports on Bruce getting involved with Arkham City, she introduces him as "millionaire Bruce Wayne", only to have him interrupt with "It's billionaire, Vicki. Millionaires are so last year."
In the epilogue, Catwoman can talk to various villains/characters. A highlight among them is her conversation with Mr. Freeze.
Catwoman: So is now a good time to talk to you about an idea I had to steal the Pharaoh's diamond from the Egyptian museum? It's really hot there and, well, all this latex really makes a girl sweat...
Mr. Freeze: (Deadpan) Leave me with my wife, Catwoman.
Her exchanges with Ivy before, during, and after her boss fight in Episode 2 are hilarious, but the one commenting on how she's controlling some of the inmates with pheromones takes the cake.
Catwoman: Hey, Pammy, here's an idea! If you want a boyfriend, how about trying the dating route? Beats this voodoo crap.
Catwoman: Well, what do we have here? Weird, out of place plants...check. Mindless, hypnotized henchman...check. The oh so subtle odor of rotten pumpkin...check. Looks like I've found the entrance to Ivy's lair.
Any fight with one of the Abramovici twins becomes this if you use the stun gun, which makes enemies flail around with their weapon when hit. Couple this with their size in a room crowded with goons, and Hilarity Ensues.
After you have capture the Riddler, you can be a jerk by standing in front of him. You can also gag/ungag Harley later in the game to hear humorous result.
When the enemies start pulling out sniper rifles, complete with laser sights, upon your return approach to the Steel Mill:
Mook: Nothin's gettin' past me.
cue Batman sneaking up behind them and knocking them out, or just plain pulling them off the ledge.
After you rescued Aaron Cash, you can ask him about Protocol 10.
Cash: Is that some kind of hemmorhoid cream?
Batman: I doubt it.
When you pursue a side mission in the Steel Mill, you come across a powerless elevator with some mooks trapped inside, trying to get it to work. Have fun listening to their panic when you use the Remote Electrical Charge to make the elevator go up and down.
The Joker phone calls. Especially when he gets mad that you won't pick up.
When rescuing the 5th Riddler hostage, one of the taunts the Riddler throws is this gem:
Riddler: Oh come now. Surely "the great Batman" can progress without cheating and looking for answers online.
Joker: He's taking you guys to pieces like a puppy in a blender! PULL YOURSELVES TOGETHER!
Batman threatening Riddler informants is pretty hilarious. Rhis line, for example:
Batman: Please don't lie to me. I just cleaned the last informant's blood off my face.
Joker explains to his gang members how he's been cured, but then compares the whole thing to the revelation of the mystery on a TV show. Then he follows that up with, "How come it all ended in a church?"
Solving Riddles in the game will reward you with little bits of backstory about what took place between Arkham Asylum and Arkham City. One of these stories reveals that Joker and Harley actually escaped before being transferred to Arkham City in an attempt to keep away from it. Instead, they stole a boat, and after being chased by Batman, wound up sinking said boat and having to swim to shore, winding up in Arkham City anyway.
Batman's dying, surrounded by assassins, but still manages to crack wise when he gets slapped in the face by Talia Al Gul.
At the conclusion of the "Fragile Alliance" sidequest to destroy the Titan containers with Bane, this happens:
Batman: I've destroyed the containers, Bane.
TYGERnote If you finish the quest after the main game, it'll be Joker henchmen instead.Mook: Hand over the Titan!
Bane:Help me, Batman! We must not allow these puppets to take the Titan!
[at least fifteen TYGER guards attack; Bane and Batman take them out in short order.]
Batman: [not even out of breath] As I was saying—
While you can complete the quest in the Playable Epilogue, it's funnier if you do it before the finale, because it means that Batman is at death's door and still easily kicks the crap out of over a dozen trained guards.
Joker: You remember Mr. Abramovici, don't you? Don't worry he's mostly arm'less.
Joker: Let's give a big hand for Mr. Abramovici. He certainly could use one.
A scene taken out of the game for being too funny compared to the dark tone: when Batman fights Penguin's shark on the raft, he was originally going to pull out a can of shark-repellent. Said can was going to contain a giant knuckle-duster to beat the shark with.
"Tell me, Mister Cobblepot, have you ever heard of the expression Napoleon Complex?" "No. What is it?" "It's nothing."
In Riddler's hideout, if you wait long enough in that one spot in the vent you can see Riddler from, he'll start talking to himself about what he needs to do to beat Batman. His spiel ends with this:
The way Batman uses the Batcomputer, without a word, to track villains while they taunt him about being untrackable. For example, when Zsasz tells Batman that his phone signal has been bounced past so many relays that he's untraceable, Batman immediately begins tracing that signal while he's talking about it. When Riddler talks about his henchmen that are perfectly deep undercover, Batman calls up a database of his known associates and makes a special bright green overlay for them before the Riddler even finishes his paragraph. Etc.
Mr. Freeze's interview tapes are mostly quite somber, for obvious reasons. However, one moment from the third interview tape stands out:
Freeze: Do you know what it is to love someone? To reallylove them?
In the mission to rescue Nora Fries, if you wait to listen to the Enemy Chatter before jumping the mooks, you can see them playing rock paper scissors, introducing things like guns and dynamite and getting called on it.
It's not only that: they're trying to have a three person game of rock, paper, scissors, and none of them seem to know how to play.
Upon visiting Museum after the end game, you can hear they discussing about what will come up next. One of them wandering if they are going to have Arkham County or Arkham Nation next. At the end they admit that both names sound stupid though.
Mook: What is wrong with the Riddler freak? Doesn't he have anything better to do than leave green question marks all over Arkham City?
It's even better when the Mook saying that is one of Riddler's "undercover" henchmen.
After the Penguin's been defeated, you come across a crowd of his mooks in the subway, getting a recruitment speech from one of the Joker's men. For maximum levels of irony, you can pop out of the grates and K.O. the speaker just as he goes on about how 'invincible' they are.
Even better. One of them, who is playing around with a mask, talks about how he will always join the stronger faction, having no loyality beyond that. Said mook is actually a Riddler henchman.
There's actually a group of unaffiliated (haven't joined any of the gangs) criminals camped out on the roof with a frozen over swimming pool who comment on various story developments as the game goes on. They even manage to survive Protocol 10. Some highlights include them debating which gang they should join up with, and joking with one another about resorting to cannibalism with one saying to another how he's starting to look like a big tasty pork chop...
Apparently one mook didn't listen to Penguin's speech on how they'll be taking over Arkham City because he was on the can.
Hearing mooks talking about their experience in Arkham Asylum during the events of the first game are always a nice call back. Especially when other inmates refuse to listen to their warnings about Batman.
Some inmates can be heard giving tips on how to survive in Arkham City, some which imply an almost Too Dumb to Live mentality among the general population:
Inmate: If you see some strange flowers or plants, it means they belong to Poison Ivy.
At one point, as Robin in Harley Quinn's Revenge, when you start a fight, one of the mooks yell "It's the Batman's bitch!"
Which becomes even funnier during Predator segments, when the same one might say "I'm sorry! I thought you were a joke! Please don't hurt me!"
Another gem from the Steel Mill, during your first time in there, two rooms before the smelting chamber, a few mooks are waiting for Batman to show up, and another one is in the next room behind a glass window, making it impossible to prevent him from seeing you take out his buddies. Rather than deal with the guy behind the window, Batman starts silently taking out the other mooks, while the guy behind the window tries to call out and alert his buddies, and while his voice isn't completely blocked by the windows (you can hear it), the other mooks are too engaged in their own conversations to notice. Cue one very annoyed guard trying to tell his buddies that Batman is right behind them while simultaneously insulting them. "Are you guys deaf?! HE'S RIGHT THERE!"
The prequel comic shows how Batman uses a nondescript boat to hide the Batboat, in order to come and go to Arkham city at will. Or so he planned - when he arrives the second time, the boat gets blown with him in it! As Batman's flying through the air from the explosion, he calmly notes that "...that worked a total of once."
Joker gets so very many great lines. After the events of Asylum, the facility's surviving guards are quite understandably pissed at him. One of them, while threatening Joker, says he and his henchmen killed lots of "husbands and fathers".
Joker: So sad...no one ever remembers the dead singles and divorcees.