When talking to Raven in the Watchtower, she may say that where she come from is the closest thing to hell, and yes, she has been to New Jersey.
In the Oolong Island alert (hard), Dr. Pyrate somehow manages to transform himself into a giant robot.
(robotic tone) I don't know what went wrong but this is freaking awesome.
If you save Mr. Freeze's goons from the cops they will sometimes pause to give you a round of polite applause.
Calculator's comment when you are heading to JSA's headquarters to rescue Sinestro:
Calculator: The Sinestro Corps recruits are homing in on Sinestro's location at the Justice Society's headquarters. Guess that's what happens when you have your address listed in the, heh, yellow pages. Really, they're listed!
Calculator himself is arguably a walking CMOF due to his Deadpan Snarker tendencies.
ALL of the Booster Gold exploration quests.
Klarion's motivation during the Halloween Event.
Klarion: I am not an emo pilgrim. I am a Witch Boy.
The Jokandroid enemy's banter combined with their Robo Speak belays how annoying they are to fight.
For heroes, there's this exchange between Giganta and Wonder Girl after you reverse the former's Grand Theft Me attempt:
Giganta: No! No! This body belongs to me!
Wonder Girl: Not anymore it doesn't, thank goodness. Because there's no way I could pull my favorite jeans over your giant behind.
The demons in Metropolis lampshading the player destroying stolen bags of money instead of taking it for themselves by telling them "Are you crazy?! That's a lot of money!"
Occasionally during the battle against Deathstroke, when he tries to kill the Riddler with a flamethrower from the weapon rack, the latter will declare "Riddle me this" and before he can finish will suddenly yell "OH GOD IT BURNS!"
As a villain, when you encounter Hawkman and Hawkgirl in Metropolis during the Gorilla Grodd quest chain the latter will comment "You should use that devolver on yourself, it'd be an improvement!", referring to the devolution device you got earlier on.
During the then-final Sins of the Father story arc in Gotham while facing the captive Titans, Beast Boy has this gem:
Gee Raven, is this what happens when you break curfew?
He receives another in the Sons of Trigon expansion:
Demons, Cultists, Villains, Paparazzi... None of them are welcome here.