During a mass break out attempt on the Raft Luke Cage vs Purple Man, who has beaten teams of Avengers before.
John Walker, former US Agent, had recently had his left arm and leg amputated. He is assigned as warden of The Raft, a prison for super-criminals. One issue has a black out that results in some of the convicts being released from their cells. Finding himself cornered and threatened, John leaps out of his chair and lays some serious hurt on the first cons to come near him, and even rips some guy's eye out using his metal hook. The fight ends with John (who, remember, is one legged) standing steadily over the knocked out body of a prisoner, daring anyone to start some shit. None rise to the occasion.
Best part, the rest of the prisoners bring him his chair afterwards.
He later catches three prisoners wandering around, making fun of Gunna. He gives them extra work to do as punishment as they sheepishly leave, one saying "Yes, sir. Thank you, sir."
John was offered high-tech prosthetics, which would have enabled him to be back in battle immediately. He instead chose to use the level of tech given to regular soldiers.
The team end up on a mission with Hyperion and the entire issue deals with fighting him. Hyperion is basically an evil expy of Superman, with everything that implies. He regards the other Thunderbolts as completely worthless, especially Ghost, and proceeds to burn Man-Thing, break Juggernaut's legs, and drown Moonstone. He's later beaten up by Juggernaut (and actually breaks his hand trying to cave Juggs' head in), blasted by Moonstone, paralyzed by Ghost, and, after a good Curb-Stomp Battle on him, burned by Man-Thing.
Moonstone: "Coward. Can't have one of these on the team. You shouldn't know fear, Hyperion. Because. Whoever knows fear..."
Juggernaut: "...burns at the touch of the Man-Thing."
On another level, the fact that Marvel kept the team's secret under wraps until the end of the first issue. Even when you know the truth and you're re-reading it all these years later, the revelation that they're the Masters of Evil—and all that entails—still really hits you.
It was considered a CMOA even back then. The first issue of the series was put into a trade with the issue of the team's first appearance due to fan request.
Likewise, tracking down the creator of Humus Sapien and letting him plot his debut storyarc, 28 years after he was originally promised.
Quicksilver gets one at the end of the Siege event. 'Perfect warrior' Mr. X has just gotten hold of 'ultimate weapon' Gungnir, and bear in mind this is a guy who killed a god before he got his hands on the Spear of Heaven. Quicksilver deals him a Curb-Stomp Battle without pausing for breath:
"I read your dossier as I crossed the ocean. You have supreme fighting skill. I'm actually not that great a fighter. You have the weapon of Odin the All-Father. I have some pieces of iron debris I found lying nearby. You're a mutant, too. You can read minds enough to predict any attack your opponent will make."
"So you will be able to (breaks elbow) anticipate every move I make (breaks wrist) and do absolutely (breaks jaw) nothing about it (breaks hand) because I (breaks other hand) am (breaks ribs) the (breaks knee) fastest (breaks other knee) man (breaks leg) on (knockout blow) Earth."
Whilst we're talking about Siege, Amadeus Cho got a really good one against Mr. X. Mr. X can read minds so that he knows how someone is going to attack him. What does Amadeus do? He throws arrows at Mr. X, doing complicated calculations so that they'll hit him in just the right spots. The best bit of it is that Mr. X can still read Amadeus's mind, he just can't understand the calculations.
When the original team's rebellion against Zemo begins succeeding, Moonstone confronts Baron Zemo personally. After a year's worth of issues where every word out of her mouth was a lie, a manipulation, or some kind of psychological trick, Moonstone finally lets out what she truly, honestly thinks about Baron Zemo while beating him to death with Punctuated Pounding:
"Let me EXPLAIN something, Zemo. Let me tell you why I undermined your leadership at every turn. I've got a pretty simple philosophy of life. You want to hear it? It's this: Don't. Get. CAUGHT! Oh, I was stupid at first - I thought my powers made me invincible...so I ended up getting a record, getting caught. I was willing to ride it out, serve my sentence and start anew - but you press-ganged me into your scheme, and there went that. Still, it was a good scheme - posing as heroes - and we made it WORK. We had it all - public support, adulation - the perfect cover to pull any NUMBER of scams - and you went and blew it over just ONE! Who CARES about ruling the world?! Who wants to do that much WORK?! We could have run this con out for YEARS before it got old! But no, you couldn't be smart - not when you could play Hitler like your idiot father!"
Examples from the Daniel Way/Charles Soule (Marvel NOW) retool:
Deadpool finally realises at the end of the mission to assassinate the Paguero crime family why he's been obsessing over a small pizza place he knows in New York, where the pizza isn't even that good. The Paguero's own the joint and use it as a hide out, and Deadpool recognised the Pagueros from their photos on restaurant's wall. He promptly guns down all three of the family's heads when they stumbled into the joint, casually outdoing years of the Punisher's work.
The Leader comes up with a plan to take out the entire team when they're on a road trip in the Battle Van. He borrows a lighter from Ross, then would use his ability to radiate gamma rays to overload and knockout him out. Leader would then the lighter set Deadpool aflame, scaring away the Venom Symbiote, and throw Ross into the blaze, having hidden the fire extinguisher. Finally when the Punisher and Elektra in the front seats are forced to stop and help, Leader would fall out then throw the team's grenades into the blaze. But even more impressively the Leader abandons this plan, as he realises his dwindling super-intelligence cannot account for every facet of this violent plan nor unpredictable human nature, and that such a plan is worthless if Mercy simply vaporises him.
Trapped in Hell, the Leader draws up an extensive contract with Mephisto to release him and the rest of the team if they help him regain the throne of Hell. He shows his genre-savviness by refusing to agree on the deal with a handshake, knowing that Mephisto would quickly turn an ambiguous deal against them.
The outcome of the deal once Mephisto is enthroned is incredible too. Mercy appears in Hell, at which point as Leader predicted she begins annihilating damned souls and ignoring the Thunderbolts. Thanks to a sub-clause in the contract Deadpool retrieves a new feather through an inter-dimensionary portal. However it's soon revealed to be an angel feather, as a horde of angels wielding flaming swords swarm through the portal. Mephisto promptly pledges eternal torture for the Thunderbolts, at which point Leader points to a sub-clause, which ensures that any retaliation would make Leader ruler of Hell. Checkmate. Mephisto gives in and sends them away.