An offhand comment by Randall to Monroe in "Ghosts" suggests that one of the Affleck brothers is now the Governor of the California Commonwealth. Actually it turns out to be the wife of one of the Afflecks.
Feared and Badass Major Neville getting his groove on with some Lionel Ritchie.
Miles tells Jason to not even think about double crossing the rebels, or he'll "smash in your pretty boy band face". Jason then asks Charlie what a boy band is.
The aftermath of Jane, an old acquaintance of Rachel's, baking two bandits with a handheld sonic weapon.
Aaron getting stuck with the shopping, while Rachel tries to decipher Jane's journal
Aaron:Two degrees from MIT, but yeah, I'll go shopping.
In "Love Boat", after Tom Neville storms into Miles's HQ:
Miles: Hey, Tom. You look upset.
"The Longest Day":
(Nora is hurriedly getting dressed the next morning after sleeping with Miles)
Miles: Hey, you gonna leave a twenty on the stand? 'Cause I feel cheap.
"Children of Men":
Neville snidely asks Aaron if he can get the group into the Tower. Aaron's response:
(holds up Jane's journal) With this I can...dick.
Monroe of all people saving Charlie's life and saying:
"The Dark Tower":
Does anyone else find the irony of the US Government in Exile being run out of Guantanamo Bay to be absolutely hilarious?
Especially given that they've got a master plan worthy of any dictatorship. If Bass hadn't been in their way, he probably would have approved, given his penchant for reciting to his subordinates what he would do to the rebels with helicopters and electrically-driven machine guns.
And in "Happy Endings", Bass remarks, "Typhus? I don't know whether to kill them or write 'em a fan letter."
And in another example of some dark humor in Bass's behavior wrt the Patriots, he decides to mustard-gas some Patriots in an eye-for-an-eye mode of thinking. Luckily, Miles and Rachel get ahead of him and figure out a better way to keep track of what they're doing, by spying on Truman.
Bass still hasn't had enough and wants to use the mustard gas to wipe out D.C. instead.
"There Will Be Blood" has Miles interactions with Titus:
(Miles has his usual weary-traveller seen-it-all couldn't-care-less attitude as he sits handcuffed)
(Titus has just been pontificating about the "better world" they live in)
Miles: Can you... you can hear yourself, right? Are you aware of how creepy you sound?
(After Titus continues for a bit)
Miles: If you're going to kill me, then do it. Just please stop talking.
Also from "There Will Be Blood"
Rachel: How are you doing? Aaron: Okay for a dead guy. A little dehydrated. Hungry for brains.
Apparently rock has, after the shutdown, become the new folk music. Reasonable enough. But it seems to be a running gag throughout the first episode of the second season that none of the people singing them can do it on key.
Monroe: I know I can never make it up, but I've got to try.