The Thunderbolts, led by Zemo, forced a Banana Republic to give up their secret atomic plans. The President Evil sent his navy, to no avail. He kept nagging that he would gather allies, go to the UN... and Zemo interrupted him, showing him and his cabinet a porn video of the president having sex with the wife of his minister (standing right next to him). What the Hell, Hero? Well, he ended the conflict swiftly, decisively, and... let's hope... without loss of life. Isn't that what heroes do?
When Fixer references Animal House mid-battle, Zemo reveals that he's seen the film, and that he was rooting for Dean Wormer.
Issue 176 (following the Dark Avengers retitle) has Man-Thing after his rebirth at the dawn of life on Earth as heard by Boomerang.
Man-Thing: Y'all tha snitches that got me my riches.
Boomerang: Why is he all thug-talking now? Does that seem weird to anyone else?
Also from Issue 176, Mr. Hyde's reaction to seeing the Watcher while time traveling.
Mr. Hyde: What are YOU lookin' at, Y' bleedin' BABY MAN!?
Upon realizing that the time traveler they rescued was in fact Dr. Doom who promptly betrays them by destroying Thunderbolt Tower, the team stares in shock and anger, vocally plotting out revenge until we get to Boomerang.
Ghost: Oh my!
Moonstone: Well, that is that. So long Thunderbolts Tower.
Centurius: If it takes a dozen lifetimes, I am going to kill Victor von Doom.
Troll: Troll... home... gone?
Hyde: I'll chew his foreign head off.
Boomerang: I'll talk a lot about evening the score, and then get distracted by stuff and never get around to it.
Ghost in a party hat.
Man-Thing and Boomerang fist bump.
Examples from the Marvel NOW series:
The 2013 annual by Ben Acker and Ben Blacker is full of good jokes, including Elsa Bloodstone mistaking Elektra and Deadpool for The White Stripes, The Leader describing his sensors' readout as "They're really calm. They sound insane. Like Kevin Spacey." and a dig at the Shawarma-eating ending of the Avengers movie, but special mention should go to this exchange between Venom and Punisher in Jotunheim:
Punisher: Let's go kill some gods.
Venom: You can't kill gods.
Punisher: I can kill whoever I want. I'm the mother ████ing Punisher.
Also from the annual: Ross declares they're going to kill Doctor Strange. Venom objects, Deadpool's all too ready to do so... and they're all stopped by The Leader - "We are unable to kill him. He's magic, we're not."
Deadpool states he's a certified notary, and thus can witness the team's contract with Mephisto.