When Mike goes on a violent spree with SIE as his handler in Marburg's mansion, she'll orgiastically start humming "The Ride of the Valkyries".
"Oh, great. It's a picture of Darcy. It says 'Mike and Sean, fuck yeah!!!' with three exclamation points."
The best part is Mike's delivery. He observes it with nothing short of deadpan contempt, except for the "Fuck yeah!!!" part, where he puts on a mocking nasily tone, then back to deadpan. It's so perfect.
You can also reply by quoting Time Cube at him. Gives double positive influence, too.
The NSA listening post in Rome. Mike's facial expressions in this scene are pure comedy gold. You'll know it when you see it.
One of Mike's possible responses when Deng orders him to get into a maintenance closet at gunpoint:
"This is going to end with me pointing out where you touched me on the doll, isn't it?"
If Mike is a veteran, while traveling through the catacombs of the ruins in Rome he'll start to hum something called "Sinister Music" by the subtitles. Mike actually sings the tune in time with the flickering lights.
If Mike agrees to let SIE...release him...and is agreeing to destroy Alpha Protocol, Westridge has some hilarious things to say about it afterwards.
Westridge: You did not just do that in my medical bay. Bet it smells like cat piss and tuna in there...
Mike getting fed up with Grigori and beating the crap out of him. It starts off as a bit shocking, but then turns darkly humorous from Mike's commentary.
Mike: (after smashing a bottle over Grigori's head) Aww, you spilled your wodka.
Sparing Brayko results one of the funniest news broadcasts in the game:
INN Newscaster: Authorities say that he will be charged as soon as he is well enough to be discharged. Mr. Brayko had no statement for the press, but while he was being loaded into the ambulance, he was heard to remark that the party responsible for the attack "an expletive American commando cowboy like the expletive offspring of Ronald Reagan and an expletive American Ninja." ... a source within the hospital stated, that, quote, "The man had enough cocaine in him to make a baleen whale see Jesus."
If you have Heck as your Handler during the endgame, you got this conversation when your chopper gets blown up.