Mega Man Zero: Zero gave Dr. Weil one of these. Dr. Weil is boasting how a heroic reploid like Zero wouldn't be able to harm a human. Zero responds by telling him he's actually not quite that noble and he's always only fought for the people he believed in and not some nebulous "defender of humanity" title, and as far as Zero's concerned, Dr. Weil's just another maniac that needs to be put down. What's particularly delicious is that Zero is not a Reploid, and that he was not necessarily constructed with the Three Laws to begin with - what with being built by Doctor Wily and all. Consider that despite not being built with the Three Laws, Zero CHOOSES to obey them of his free will. Him deciding to kill Weil was actually in compliance with Law Zero, which is essentially a threshold law designed to protect large numbers of innocent people from the depredations of someone like Weil.
There's also when Weil is gloating to Zero about how a reploid could never understand that joy he's experiencing of controlling all the Reploids in the world. Zero replies by saying that he doubts that most "sensible humans" could understand either.
In Covenant, Rasputin, facing down Yuri in his Amon fusion, simply calls him "Demon!", to which Yuri-as-Amon responds to by gathering energy and proceeding to punch Rasputin out.
Even better was the scene just before the battle with Nicolai possessed by Astaroth. After Astaroth rants about his intention to destroy the world, Yuri asks him for a favour. When Astaroth asks him what it is, Yuri says "I wish you'd shove it. You know where." The ensuing silence is incredibly satisfying.
In Star Wars: Knights of the Old Republic, an optional piece of dialogue between Republic soldier Carth Onasi and Mandalorian Canderous Ordo starts with Canderous asking Carth what battles he had fought in during the Mandalorian Wars. Carth replies that he prefers not to dwell upon the horrors of war. Incredulous, Canderous replies that he would have thought that a fellow warrior would have understood the glory found in battle. This is apparently one of Carth's BerserkButtons, as he angrily snaps back he isn't a warrior, he's a soldier, in an awesome Take That: "Warriors conquer and enslave, they prey upon the weak. Soldiers defend the innocent, mostly from warriors." Canderous snarks that Carth must tell himself that every night so he can sleep. Carth responds by asking Canderous what that Mandalorian code means when they lose, "y'know, like you did against us". Canderous fires back that the Republic had the advantages of more ships, more troops and the Jedi, and that the clans still nearly won. Carth asks him if he tells himself that every night so he can sleep. It's a SUH tennis match.
A rather amusing one in Knights of the Old Republic. Normally you cannot take Bastila with you on Korriban, however there are intact scenes and dialogues that can be activated with a mod. One of these has you learning of the Sith temples. Bastila begins to comment when she is sharply cut off.
Done in Kingdom Hearts II when Xemnas tries a Break Them by Talking on the heroes about how he had no other choice than to commit the actions that he did, only for Sora to say "Give it a rest! You're Nobodies. You don't even exist. You're not sad about anything!" Xemnas then laughs and confirms this.
Riku delivers another Shut Up, Hannibal! in that scene when Xemnas asks the heroes why they considered Organization XIII to be an enemy: "That's simple. It's because you mess up our worlds."
Riku in Chain of Memories, just before the final boss when Ansem tries to tell to him that he's irrational for accepting the Darkness in his heart but not Ansem... His response? (Foreshadowed by the fact that Riku has constantly shown an ability to actually smell people's auras).
Riku: Wrong. The truth is... you just really stink.
In Re:Chain of Memories, courtesy of voice acting cutscene and Riku drawing his blade halfway through.
Riku: That's not it. The truth is... *summons Soul Eater* I just can't stand your foul stench!
Done in Kingdom Hearts II twice, when Sephiroth tells Cloud to give in to the dark side and Cloud literally tells him "Shut up." The first time, it's in the middle of a war and Cloud is kind of trying to focus. The second... notsomuch
The first game- Sora for the first time fights Maleficent. Before the battle she begins to rant about how nothing can stop her now from conquering the universe. Sora responded by telling her "We'll stop it! After comming this far, there's no way we're gonna let that happen!". Maleficent didn't take the challenge well.
In 358/2 Days, Roxas pulls this off... against Saïx... in a three-line conversation!
In Assassin's Creed I, Majd Uddin attempts to give Altair a Not So Different speech about how it feels to hold the life or death of someone else in your hands. Altair's response is to say he's learned what happens to those who elevate themselves above others, and then stabs him in the neck.
However, it's horribly inverted in the game. You must listen to every target's speech in an Unskippable Cutscene - both before and after the assassination.
From System Shock 2, delivered by the Soldier, the main character, to SHODAN, the villainous computer system:
SHODAN: I don't understand... how could you have done this? You weren't meant to be so important... and now you think to destroy me? How dare you, insect? How dare you interrupt my ascendance? You are nothing. A wretched bag of flesh... what are you, compared to my magnificence? But it is not to late... can you not see the value in our friendship? Imagine the powers I can give you, human. The cybernetic implants I gave you, were simply toys. If I desired, I could improve you... transform you into something more efficient. Join me, human, and we can rule... '''together'''. Soldier: ... Nah. (shoots SHODAN)
It is worth noting that this is the only time the protagonist speaks in the entire game, to amplify the awesome.
In Fable II, in the final confrontation with Lucien, when he launches into a tirade about why he became a villain, you can shut him up at any time by shooting and killing him. If you don't, eventually Reaver will get tired of Lucien's rant and kill him for you.
In The Elder Scrolls IV: Oblivion, when the protagonist finally meets Big Bad Mankar Camoran, the villain launches into a gloating speech...which the protagonist can end at any time with an attack.
In Killer7, after the stylish duel between Dan Smith and Curtis Blackburn, the latter tries to justify what he does with the empty bodies of the girls he sells to the organs' black market saying things like "Everyone should have a hobby after retirement" and "All I ever wanted was to shed a light in my life". Dan, his old partner and the one with the least moral issues in the Killer7 syndicate, is visibly disgusted, and after saying "Trying to die in style? Gimme a break, you sick old man!" shoots a lever that gives Curtis the same treatment he gave to the girls whose bodies are hanging up in the corridor as trophies.
In the Game Boy Color version of Rainbow Six, after John Brightling defends his plan to spread a virus across all of human civilization by introducing it at the Sydney Olympics by saying "At least my way, the animals would have survived," one of the members says "This way everyone survives," absent from the PC version.
Mondo Zappa, from Killer is Dead, is a Consummate Professional who has little patience for his targets talking his ear off. For the most part, he warns them that he's a busy man and proceeds with the fight. During his final fight with David, however, he straight up stabs him, telling him "You talk too much!"
Mithos: It's because we couldn't do that! That I... we... wanted a place of our own! Zelos: Uh-uh. Sorry, but don't act like you're the only victim here. It doesn't even come close to justifying all the things that you've done.
In Tales of Symphonia: Dawn of the New World, the final boss does this to you while the heroes try to convert him if you let the battle conversations go on long enough. Though he's not exactly the villain of the piece. He actually does it about 5 times in the conversation, each time telling the heroes that he doesn't want to hear what they're saying, that he just wants to kill them, but the end of it has the most "SHUT UP!" about it:
Emil: I won't die. The courage you taught me spurred me on. We'll make sure that this world doesn't turn into a demonic realm!
Richter: Silence! I won't be distracted by your appearance any longer!
In Tales of Destiny 2, Elraine put Judas in a Psychological Torment Zone and tries to get him to make a Deal with the Devil via forcing him to relive his betrayal of his friends and death over and over in between Hannibal Lectures. When she offers him a chance at redoing the past and getting both Marian's affection and recognition as a hero, he laughs at her, saying she'd never understand his motivations for his past actions, that he has accepted responsibility for those failures, and that he is no longer Leon Magnus, but Judas, and he'd rather take any curse than serve her.
In SD Snatcher, the master Snatcher is lecturing Gillian on how it's plan will succeed and snatchers will destroy the humans. Gillian's response? "No way, dickhead! Not when Gillian Seed is alive!!".
Scirocco: By averting that Colony Drop, you wasted a good chance of getting rid of all those fools whose souls are bound by gravity. Kouji: Oh, don't give us that crap! We won't let you even touch the Earth we live in! Scirocco: The lives of those who cannot understand genius are of no importance to me, since genius surely is the driving power of the world. Daba: This Scirocco guy is just as bad as Posaydal... and I'm afraid the same mistakes will be committed in this universe as well. Kamille: Scirocco! We're not letting despicable people like you, who laugh at others from their comfy seats, get away scot-free! (the heroes proceed to pummel the living heck out of Scirocco and the Titans)
In Advance, a similar exchange occurs between the Londo Bell and Evil ChancellorHaman Kahn during her attempted Axis drop. At the heroes' protests, Haman says that she's only doing what is bestfor mankind's future. Banjou Haran, the protagonist of Daitarn 3, retorts that she, and only she, decided it, and that nothing gives her the right to commit genocide for her supposed higher ideals.
Alpha and OG timelines have probably the most memorable user of that trope:
"Shut up! And listen! My name is Sanger, Sanger Zonvolt! The sword that cleaves evil!"
In Shin Super Robot Wars, Londo Bell receives an unexpected communiqué from, of all people, the Neo Zeon - in particular, from Char Aznable! Gomez takes the call, asking whether the rumors of Char's turning traitor on mankind are true. Char allows that he's aiding the aliens, but says that he hasn't sold out humanity. Romelo doesn't buy that, but Char asks the Londo Bell what they think awaits at the end of this fight. After all, the Ze Balmary Empire possesses such incredible technology that they've been able to come all this way just to take over the Earth. He figures that Londo Bell's foolish resistance is only going to enrage the more, which is why Neo Zeon jumped at the chance to help the aliens, as the one and only means to ensure a future for mankind. Amuro Ray interjects and tells Char to shut up. Amuro points out how Char loves to prate on about justice based solely on his own narrow views. He asks what value a peace founded on the sacrifice of numerous human lives could have, and challenges Char to stop treating other people's lives like toys for once. Char thinks Amuro is full of it, claiming that mankind's history shows that people are happiest when ruled by the strongest leader. He thinks Amuro is incapable of grasping the larger picture, accusing him of myopically leading people even deeper into danger and then having the gall to question his lofty perspective. Amuro fires back that capitulating to the aliens and therefore making human kill human cannot be correct. Char asks whether Amuro thinks that fighting until no one is left can really make mankind happy, and Amuro points out that mankind's defeat is not yet a foregone conclusion. Kouji Kabuto finally interrupts, pointing out that there's no way to know that until they try. Shinobu Fujiwara goes further, angry beyond measure at people like Char who debate outcomes without lifting a finger on their own. Char figures that there's no common ground between Londo Bell, and informs them that he'll show them no mercy, which is just fine with Shinobu.
In Skies of Arcadia, the Silvite Elders spend a good few minutes explaining how horrible, greedy, miserable, etc humanity is and uses it to justify unleashing the Rains of Destruction again. Although you are given a choice in how to respond, the one that increases your Swashbuckler Rating and is in-character for Vyse is the one where he tells them to shut up and exclaim loudly that they have no right to commit genocide just because the world doesn't live up to their standards, with double burn points for the fact that they've willingly isolated themselves from said world and could have chosen to do something more constructive about it all this time, but never did.
The best part about this is it convinces them to take action, by ramming their whole base into the barrier around Soltis, shattering it.
There are several of these in Sonic and the Black Knight when Sonic confronts Merlina, who explains that the only way to save Camelot from its tragic fate is to use the power of Excalibur's Scabbard and the Underworld to make it eternal, only to have Sonic reply "What good is a world that goes on forever!?" The conversation even ends with this great exchange between the two characters:
Merlina: My sorrow at its ruin runs deeper than the depths of the underworld... do you not understand? Sonic: No! And I don't want to!
From the fight with the hobo Mini-Boss Oscus: "You figure the best way to stop this speech is to hit him."
Against the Naughty Sorceress's second form: "You found me beautiful, once..." she says. "Honey, you got real ugly. Yo, she-bitch! Let's go!" (It's also a Shout-Out to Army of Darkness.)
Persona 4 has this happen after the revelation of the killer. In a long-winded spiel, the killer explains that the TV world is the best thing to ever happen to anyone. The heroes' response?
Yosuke: Favored by the world, my ass. I'm just gonna say it flat out. You're just a worthless criminal!
Also deconstructed — when your inner Shadow Archetype begins revealing facts about your inner character you'd rather not hear, despite being utterly true, denying it and asking it to Shut Up, Hannibal! is a very, very, very poor idea. The thing that eventually defeats the shadows (after the inevitable Boss Battle) is to do exactly the opposite and own up to their claims, using the knowledge that you have a problem as a foundation for improving yourself. It also gives you superpowers.
In the Mass Effect 1 DLC mission "Bring Down The Sky" you're given the choice between saving the hostages and letting the terrorist escape or killing the terrorist and letting the hostages die. If you pick the latter, once you're done dispatching his mooks you come up to him. Picking the Renegade option leads to this exchange:
Balak: I gave you the chance to save them and you turned it down. Who's the real terrorist here? Shepard: You are. But you're dead. (shoots him)
Another nice one between Shepard and a krogan: Uvenk at one point is going on about how Grunt does not deserve to take part in Clan Urdnot's Rite of Passage, insulting him all the while, and Shepard can take a page from Wrex's book and headbutt Uvenk in the face. Uvenk is more surprised than at all hurt, but the other krogan watching find this hilarious.
Another epic one occurs in the Kasumi DLC. You're in the villain's vault full of priceless artifacts to steal back something, and a giant hologram of his head appears to tell you that he knew you'd come and now he has everything he needs and blah blah blah. A Crowning Moment of Awesome invokes this trope when Shepard checks their pistol while Hock blathers on, levels it at a priceless vase and calmly blasts it to shards. "Do I have your attention now?"
At the end of the second game, if you choose not to give Cerberus the Collector Base, you get to perform one on The Illusive Man as he rages on you for not "securing human dominance" as he puts it.
Also subverted in Lair of the Shadow Broker. After defeating Tela Vasir, she ekes out a devastating "The Reason You Suck" Speech with her dying breath about Shepard's hypocrisy in working for Cerberus and (depending on choices) remaining a Spectre, while calling out Vasir for working for the Shadow Broker. She also dies before Shepard can respond, giving her the last word.
Speaking of Shadow Broker, Liara gets one later in the mission. Against the Shadow Broker himself, no less. The Broker is trying to scare Liara by telling her he knows her secrets. She responds by figuring out that since he's a yahg, he must have killed the original Shadow Broker and taken his place some 60 years ago, finally ending by calling him a slave and a pet - the most devastating insult in yahg culture. He doesn't take it very well.
Equally awesome is the Paragon interrupt during said rant: Shepard points out to the Reaper that whatever race it has been created from eons ago is long dead. The Reaperpromptly shuts down.
In the Extended Cut DLC, Shepard can try to do this to the Catalyst by refusing its choices and possibly shooting at it. This leads to the Reapers winning in this cycle, but losing in the next.
Grom Hellscream in Warcraft III gets quite possibly the most bad assed one ever. After the gigantic Pit Lord Mannoroth, who wields a double-ended pike that's as long as two men are tall, defeats Thrall effortlessly, he gives Grom a short version of a Not So Different speech. Grom responds by roaring, charging at Mannoroth, killing him in one hit, and then being mortally burntin the ensuing firestorm. He goes with a smile on his face, pleased that he managed to free the Orcs from their corruption for good.
Grom: The blood haze has lifted... the demon's fire has burnt out in my veins... I have freed myself... Thrall: No, old friend. You freed us all. (roars in mourning of Grom)
Immediately after killing Aeris in Final Fantasy VII, Sephiroth starts to give his umpteenth villainous speech about how everyone will live again as part of him when he absorbs the lifestream and becomes a new god... and Cloud achieves a brief Crowning Moment of Awesome when his text box pops up and actually covers up most of Sephiroth's speech with the words "... Shut up."
Even the Turks get one of this in on Don Corneo in Wutai, after Cloud And Friends and the Turks team up to release Yuffie and Elena from Corneo's clutches. Mostly they turn his "Reason You Suck" Speech against him. And it is awesome.
In Final Fantasy IX, Garland tells Zidane to destroy Gaia, since he's an Artificial Human created for exactly that purpose. Zidane refuses, obviously, but when Garland tries to push he delivers an amazingly snappy and spoilertastic comeback:
Garland: Regrettable. I thought your soul would be a perfect choice for the new Angel of Death.
Zidane: I am the new Angel of Death. Yours!!!
A variant takes place in Wild ARMs 1, when Zeikfried ensnares Rudy's arm with a cord to try and drag him into a black hole, and goes on about how the two of them are Not So Different, even calling him "brother" and saying that if he goes down, he'll take Rudy with him. Rudy's a Heroic Mime, of course, so his action speaks a thousand words — he shoots/cuts off his own arm, freeing himself and letting Zeikfried fall into the black hole. The variant, of course, being the fact that Rudy hurt himself instead of Zeikfried...
In Silent Hill 3, what is Heather's reply to Leonard after the zealot claimed that a heretic like her only deserves a gruesome death? "Is every person here a mental case? [...] Well, I suppose you're not a person anyway." and then she proceeds to shoot him in the face with a shotgun.
Heather has a talent for telling Hannibal to shut up. She repeatedly smacks down Claudia's elaborate speeches about how the world needs her rather twisted brand of salvation, with lines like "you self-righteous witch, nobody asked for your help!"
In Baten Kaitos Origins, after the Duel Boss battle, Baelheit tries to justify his attempts to blow up floating islands by stating that people's reliance on their powers of hearts will cause them to repeat the War of the Gods, the massive calamity that destroyed most of the world and caused islands to float in order for people to survive. Sagi's response? He states that Baelheit's reasoning is all self-righteous crap and that Baelheit can keep all the excuses. And then Sagi proceeds to knock Baelheit to the ground.
Save your monologue for the next world. Sagi, let's finish him.
The Legacy of Kain series uses and averts this - both Raziel and Kain have about a 50/50 tendency of either listening to the tirades of Moebius and the Elder God or telling them where to stick it. The chances of doing the latter increase as soon as they find out how to neutralize Moebius' paralyzing staff or escape from the Elder God's realm.
Len vs. White Len in Melty Blood gives us one of the very few times Len ever actually says anything. White Len is sneering about how she is the voice and mind of Len and how much Len sucks and should just go away and die or something. Len tells her to shut up, she has her own will. Since she's currently the PC, she obviously wins.
Colonel Hakha in Killzone delivers one to General Lente with a shotgun shell after the latter reveals that he had the former's brother killed. Delivered later to General Adams if you play Hakha in the final level, when the former delivers a line about how they're Not So Different.
In Tales of Vesperia, Phaeroh gives a speech saying how Estelle's death is necessary for preserving the world, and how finding an alternative way is pointless. Yuri cuts him off and states the fallacies of Phaeroh's logic in a true Crowning Moment of Awesome.
While completely ignoring Yuri's use of the exact same logic for the killings of Ragou and Cumore.
A better example happens later, when Alexei is explaining his motives at the Shrine of Zaude. The entire party, including his former henchman Raven, take turns telling him to shut up.
Most of the boss battles in Final Fantasy Tactics consist of you shutting up the enemy via superior firepower, as they will at various points through the battle taunt you about their supposed superiority until you defeat them. One of the most satisfying deliveries of such a Shut Up Battle is against Algus/Algrath.
Elmdor shuts up Barinten/Barringten by having his assassin toss him to his death when he confronts Rafa on the rooftops of Riovanes Castle.
Which of course is a reference to her original game where she gives a similar speech during the final battle and gets struck down mid-sentence.
Lightning in Final Fantasy XIII does this to Orphan just before the finalfinal boss fight.. He only manages a creepy laugh and three words before she gives him a lecture that lasts about a minute. But it is an awesome minute.
"You don't believe in anything. You gave up on life before you were even born. Sat poisoning Cocoon from the inside, waiting for someone to come and destroy you. Sure, you think the end of the world is salvation. All you care about is death's release. So take it, and leave the rest of us alone! We don't think like that. When we think there's no hope left, we keep looking until we find some. Maybe Cocoon is past saving, but it's our home, and we'll protect it or die trying! We live to make the impossible possible... that is our Focus!"
Luigi: Hey! Stop messing around and fight us for real!
S.W.I.N.E. has an interesting version: Irontusk is about to escape in his zeppeling and he's raving about how he will return and crush the rabbits... until his zeppelin is blown in two by a Genre Savvy rocket tank. Shut Up, Irontusk indeed.
The last chapter of Half-Life 2 begins with Gordon hearing the end of a speech Breen is making to Eli about the future of humanity and all the glorious things the Combine can show us. Eli responds with "What I've seen is also beyond words: Genocide! Indescribable evil!", and likely would have continued in that manner had he not seen Gordon was also a prisoner.
A player-controlled version comes later when Gordon is fighting through the Citadel. Breen shows up on various screens and loudspeakers along the way, each time taunting Gordon, telling him how he was always a minor presence at Black Mesa, how everything Gordon's done since has caused more killing and destruction... if you as the player are so inclined, Gordon can simply destroy any of these screens or speakers along the way to shut Breen up mid-speech, all without Gordon ever saying a word.
In The Godfather game, various enemies will try to give a Motive Rant if you interrogate them. In order to do so, you need to be grabbing them. As a result, after they finish speaking you can proceed to off them however you like.
In a somewhat gentler example, one of your other options in that scene is to tell Morrigan severely that everyone deserves respect...even her.
A Human Noble PC gets an even better one when facing down Arl Howe, the man responsible for betraying and killing your family in the beginning. At first, he mocks you about how he made your mother and father suffer before killing them and burned your sister-in-law and nephew's bodies on a trash heap, but then you get the chance to verbally tear him to shreds, basically calling him a coward and showing him that all he's done has only made you stronger and more determined. His reaction is priceless.
Arl Howe: "There it is, right there. That damned look in the eye that marked every Cousland success that held me back. It seems you have made something of yourself after all. Your father would be proud. I, on the other hand, want you dead more than ever..."
At the end of the Godlimations flash RPG Amea, The Master Eye claims that it stealing the people's eyesight and replacing it with the "True Light" has brought them happiness and peace, and points out that all of them, even Amea herself, had chosen to follow him. Amea simply responds that the "happiness" the Eye has brought to its followers is all a lie, and that its better to face the true state of the world, no matter how bad, then to hide yourself behind the lies of a false god.
Fatman, one of the bosses in Metal Gear Solid 2, is convinced that he is a Mad Artist, who will be remembered through history as the greatest bomber and demoman in the world. Raiden interrupts his little speech, snapping "You're nothing but a common criminal, and that's the only way people will remember you!"
A silent version turns up in Portal 2, where Wheatley goes into a long speech, trying to convince you to take a "death option". You can create a portal network that launches a mine at the monitor they're speaking from at any point in the speech, prompting the response of "I'll take that as a no".
At the end of Sly 3: Honor Among Thieves, Dr. M tries to convince Bentley that the Cooper family are a bunch of self-centered greedy attention grubbers, and that he and Bentley are the same due to them both being the technical minded members of the team, Bentley responds saying that they are all brothers, and that's why he and Murray are going to stop him.
The sci-fi submarine combat game Aquanox has a pretty funny one. Towards the end of the game, the hero Flint confronts the leader of the Crawlers, the setting's Usual Adversaries. The Crawler Leader gives a big, incredibly melodramatic speech about how he's going to wipe out human civilization and eat everybody. In response Flint simply quips "Soooo... you write your own material?".
Before the penultimate story battle in Disgaea 3, Super Hero Aurum goes on about how a hero only exists when there is evil to fight, and is useless otherwise. Mao, having sat in the back and listened to the rebuttals of the others this whole time, has finally decided that he has had enough crap.
Mao: ...Hmph. I stay quiet and listen, and you continue to blab. It was only you alone that wanted any of this. Was a hero such a dinky existence that you couldn't shine without an enemy? Were you so pitiful that you had to watch out for what the people thought, and be afraid of being forgotten? Is it a hero's job to raise an enemy just to make yourself look greater? Did you want praise for your efforts? Aurum: You... ! You dare insult me, the Super Hero?! Mao: Shut up! You're not a hero, nor human! You're just miserable evil who's clinging to distorted justice! The human world is what you should've been protecting! The moment you stopped, you lost the right to be a hero! "A hero must act with courage to protect that which is precious!" Aurum: Huh! That's...! Mao: For those whom you must protect, for things precious to you, a hero squeezes out every bit of courage he has... Yes... A guy like this Almaz is the true hero, don't you think!?
In Ninja Gaiden III: The Ancient Ship of Doom, Ryu Hayabusa gives one to Clancy after the latter offers him the chance to join him in the destruction of the human race, saying that he just wants to protect the Earth from the damage that humans cause. Ryu's response?
Ryu: No reason can ever excuse the destruction and slaughter of mankind. The only thing that's going to get destroyed is you and this dimensional warship!
The Legend of Zelda: Twilight Princess has Zant claiming that he should have been the rightful ruler of the Twili instead of Midna and her "useless, do-nothing royal family". One ass kicking at the hands of Link later, Midna tells Zant that the reason the Twili didn't go along with him was because they knew he was a power hungry psychopath.
Persona 3 saw Junpei cutting Takaya short, as he rants on about how death and the Fall are the light to guide humanity out of the darkness:
Junpei Iori: "I'm not dying so you can have a friggin' night-light!"
Nearing the end of Gears of War 3 after Marcus' father had committed a Heroic Sacrifice and died right in front of his son. Queen Myrrah, defeated, approached the gears and gloated to Marcus how all he had ever done is find ways to kill lots of people. Marcus simply stabbed her and said:
Marcus: This is for Dom and all the others you have killed, you bitch.
Done earlier in the boss fight if you keep it going long enough. As Myrrah tries to stop Adam's Locust killing machine, she goes on a rant that humans are inherently violent and genocidal, prompting her Locust to act the same way to defeat them. How does Marcus react to this insult to humanity? Does he deny it as not our nature?
Spider-Man: Explain it to my rapidly retreating backside!
Kerrigan in StarCraft II: Heart of the Swarm, being a former villain herself, is unsurprisingly good at doing this. She gets an especially epic one toward the end of her campaign, where she has invaded Korhal and is about to finally get her revenge on Arcturus Mensgk. Mensgk, right before the battle starts, delivers an attempted Badass Boast where he plays on his Villain with Good Publicity status, portraying himself as the heroic savior of humanity while taking advantage on the role she played as the Queen of Blade. Kerrigan's answer?
Kerrigan: "What a nice speech, Arcturus. I shall write it on your grave."
BlazBlue toys with yet another trope. While Terumi is glad to drop into breaking speeches and Hannibal lectures, he will drop that protocol if he lays eyes on Makoto and attempt to kill her on sight. Not that he didn't try - at the end of her CS Arcade run, she starts grilling him on his plans for Noel, only for him to go into a spiel on how being created by human hands are tools of human ambition - this includes both Noel (a Prime Field Device-slash-Murakumo Unit originally designed to destroy the Master Unit) and Makoto (a beastkin descended from those originally designed to fight humanity's wars and the Black Beast). Upon hearing that last bit, Makoto slams him with this trope, sternly declaring that beastkin were never tools. While it doesn't shut him up, it does cement in his mind that casual trolling just isn't going to cut it with her. * Keep in mind this is the harshest reaction he got out of her after slamming both her primaryand secondaryberserk buttons at full force. Manipulation doesn't work; this is the second occasion she held her ground against him, which rules out torture; and using Ouroboroswould fry Relius' plans. Needless to say his patience with her just hit an all-time low.
In Project X Zone, Jedah Dohma gets himself on the receiving end of twoShut Up, Hannibal! moments. The first one is at Prologue 3 where SangerZonvolt does not let him finish his speech and declares that Jedah's evil and he needs to get cleaved/smote. The second one is when he makes the party tearfully accept salvation, Dante calls him out that he doesn't even know how to cry and that he's gonna kill him, end of story.
Apollo: "No, you twisted samurai! You stop your gabbering for once and let me finish!"
The 2009 Bionic Commando gets a hidden one in the fight with Groeder. Sit through his speeches once during the boss fight, then die in whatever fashion you see fit. The fight restarts, and Groeder goes on his rant again - but this time, you and Spencer have the option to tell him where to stick it.
In Shin Megami Tensei IV, the answers you give to the Boss Banter can potentially have this effect, throwing back a boss' words at him or ridiculing his posturing.