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The thugs in the courthouse, if you go back later as Catwoman. One of them mentions that Two-Face disappeared, but that it "was all part of the plan." Another thug then asks him whether getting wiped around the floor by Batman was part of the plan, and he replies, "Yeah, I guess it was."
I've platinumed the game and even still I've only heard this said once and I've looked everywhere for this one line because it really garnished a chuckle out of me.
One of the inmates says to the effect "they've got Arkham Asylum and an Arkham City now? what's going to be next, Arkham PLANET?"
I wish I could find it again and listen to the conversation. Most of the time I'd drown out the chatter, but sometimes they'd say something that I'd think about afterwards and go... wait, did he say what I think he said!? ^_^