Jack:Shoot the hostage. Harry: What? Jack: Take her out of the equation. Go for the good wound and he can't get to the plane with her. Clear shot. Harry: You are deeply nuts, you know that? "Shoot the hostage"... jeez...
If a bad guy is using a hostage as a Human Shield, the expected response is to Put Down Your Gun and Step Away. Some characters have different ideas...
A sufficiently skilled hero will just Shoot The Hostage Taker. If the hero is less skilled but relatively nice, they'll just shoot the hostage in the leg, either to stop the bad guy from being able to take them with him, or just to get them out of the way so they have a clean shot. If the hero is a particularly dark Anti-Hero or on a revenge fueled bender, they might just shoot the bad guy through the hostage (and then possibly regret it later).
As a note, a shot in the leg can be fatal, especially if the time between the shooting and presumable paramedic arrival on-scene/transport to hospital takes as long as it seems to in most movies, so this usually wouldn't work in reality.
If a hero tries to use a hostage, there a high chance the Big Bad will do this - without bothering to go for a non-lethal shot.
Can overlap with Trial by Friendly Fire if the hostage is an ally actively opposing the villain. Contrast with Bulletproof Human Shield.
Also see Hostage Spirit Link, a form of Videogame Cruelty Punishment where the health and/or fighting ability of the player is diminished if he decides to put a bullet through the hostage's head instead of save them.
WARNING: High risk of spoilers.
In the first anime, Alucard warns Seras ahead of time (using telepathy so the villain can't hear them) and asks for permission to take the shot and vampirize her, and takes the shot when she agrees.
In the OVA and manga he just asks her if she's a virgin. When she screams "Yes!" he takes the shot (in the Hellsing universe, vampires can only be made by drinking the blood of a virgin member of the opposite sex), then offers to turn her while she's dying.
In the second Detective Conan movie we see Ran's father once shot her mother for this reason, although it took Ran and the police officer who told her about it a while to figure out he was anything other than a bad shot. Actually this was made to save them, as the trauma of being shot at makes the hostage dead weight, to where the criminal will often just let the hostage go rather then struggle to carry them.
In the same movie, Conan shoots Ran in the leg for exactly the same reasons. Both merely just grazed them.
Lina Inverse of Slayers doesn't just shoot the hostage, she launches a Dragon Slave at the both of them.
In Akumetsu, when Perfect One fires into the researcher to kill Jinguuji but his aim is so perfect that the bullet does not pierce any of her vital organs, leaving her alive and still kicking while Jinguuji bites the big one.
Early in the JoJo's Bizarre Adventure story "Diamond is Unbreakable", a man possessed by Angelo's Stand holds a woman at knifepoint and threatens to kill her if anyone tries to attack him. Josuke solves this by punching a hole through the woman to get to the crook. It helps that Josuke's Crazy Diamond Stand can instantly restore anything to its original state, so the woman is unharmed. He uses the same tactic later to remove the Stand from his mother's body.
Earlier during the Chunin exam, Ino takes possesion of Kin and claim to her partners Dosu and Zaku that if they kill her, Kin would die with her. Ino has to undo her jutsu when the two makes clear they don't care.
In Sword of the Stranger, when the Chinese learn that the daimyo has kidnapped one of their own to find out what they're up to, they kidnap the daimyo. When the daimyo's general and his samurai attack, the Chinese use the daimyo as a hostage, thinking this will dissuade the samurai army. However, the daimyo's general is a Dragon Ascendant, who surprises the Chinese by ordering an archer to shoot the daimyo before opening battle.
Gunslinger Girl. Terrorist leader Dante is using Rico's handler Jean as a Human Shield, knowing that the cyborgs are brainwashed to protect their handler at all costs. Earlier however Jean made it clear that both their lives were expandable in order to kill Dante (Dante had planted the car bomb that killed Jean's parents, little sister, and fiancee), so Rico fires a 20mm anti-material shell through her handler's chest after Jean orders her to fire regardless.
Dragon Ball: Goku once faced a villain who held a hostage who told Goku not to care about his life. However, the hostage had a change of mind once Goku made it clear he'd respect the hostage's "request".
One Piece: The CP9 Agent Rob Lucci's backstory includes him being sent to deal with pirates that had take 500 of a country's soldiers hostage. As Lucci is a One-Man Army, he could have immediately beaten all the pirates himself, with few of the soldiers dying. Instead, he lets the pirates catch him so he'll be taken to the hostages. Once there, he kills them all himself, reasoning that those soldiers failed to protect their country and thus were worthless. After that, he kills all the pirates as well.
In Gundam Unicorn when the crew of the Nahel Argama learn that one of the refugees they rescued is actually Mineva Lao Zabi, the fugitive princess of Zeon, they try to use her as a hostage against the Neo-Zeons attacking them. Resident Char Clone Full Frontal coldly informs them that, princess or not, their current mission is worth far more than the life of one girl and orders his men to open fire anyway. Possibly a Take That to a similar incident in Gundam SEED where the antagonists did back down from putting their princess' life at stake.
A stabby variant is shown in this short story on Magic: The Gathering's website. Skipping to the end, Iizuka the Ruthless, ronin warlord, finds his son being held as a human shield by a bandit leader. Iizuka resolves the situation by skewering them both — he can have more children, after all — then orders his men to the attack.
In the comic book series Preacher, during the Saint of Killer's Start of Darkness miniseries, the man who doomed the Saint's family takes a prostitute hostage. The Saint shoots and kills her to get her out of the way... Expending his last bullet in the process and leaving him incapable of finishing off the villains, who promptly kill the Saint in return. And then there's the little issue about spilling innocent blood, which cements his damnation.
Early in The Maxx, the villain Mr. Gone takes a hostage, threatening to kill them if Maxx didn't give up. Maxx proceeded to crush the hostage's head. It turned out it was just a mannequin, but neither of them knew that.
Mr. Gone:(outraged) You killed my hostage... you killed my hostage.YOU KILLED MY HOSTAGE!! (blam) Never... do... that... again.
Seen in the comic book Green Arrow, where it only helps the protagonist. Assassin Constantine Drakon had shown the ability to catch arrows midflight, no matter how many were shot at him at once. Then he took not-yet-superheroine Mia Dearden hostage. Green Arrow Connor Hawke just shot him through her shoulder.
In an early issue of Marvel's G.I. Joe run, the Joes take Cobra Commander hostage to escape his hideout. Colonel Brekhov of the rival Oktober Guard shoots Cobra Commander to prevent the Joes from escaping. It turns out though CC was a body-double and the heroes get to get away anyway.
In one issue of Those Annoying Post Bros, the original Caroline is kidnapped, in spite of that fact that Professor Ed made thousands of clones of her to prevent that. Henry tries to rescue her. When he fails, Ron Post just kills her instead.
In one issue of Ultimate X-Men, Magneto grabs Havok to use as a hostage to force the X-Men to stand down. Cyclops doesn't hesitate for a second to fire an optic blast through Havok to hit Magneto. Of course, as brothers, Cyclops and Havok are naturally immune to each other's powers, so Magneto takes the full force of the hit while Havok is unscathed.
Another issue inverts the trope by having Cyclops himself taken hostage. He shoots Colossus, bounces the beam off of him, and knocks out the gunman.
In Rawhide Kid: The Sensational Seven, the Kid is face to face with Big Bad Cresto Pike, who is holding two hostages in front of him: Wyatt Earp, and the Kid's father. Without hesitation, he shoots them down non-lethally before fatally shooting Cresto. He's a Western hero, he has Improbable Aiming Skills as a matter of course.
In Terry Pratchett's novel Monstrous Regiment, Sergeant Jackrum shoots at an enemy soldier holding Lieutenant Blouse hostage, taking off a bit of Blouse's ear in the process. Jackrum's unnervingly casual about it... "Wouldn't be the first officer I've killed, neither..."
Another example, at the end of Hogfather. Susan ends up with the Big Bad hiding behind her elderly grandfather. She's armed with a poker from the fireplace. She hurls it through her grandfather and into Teatime. Makes more sense given her grandfather is somewhat thin.
In James Swallow's Warhammer 40,000 novel Faith & Fire, the Back Story tells of Saint Celestine and how a soldier serving her was once taken hostage. He shouted for her to kill the enemy anyway, and she threw her spear. He was mortally wounded — but didn't die, in the Miracle of the Wound. The religious ceremonies at the beginning of the novel are in honor of this miracle.
Variant in one of the Star Trek: New Frontier books, in which maverick captain Mackenzie Calhoun takes The Kobayashi Maru test. His response to the no-win scenario in which your ship must face an unbeatable number of Klingon warships in order to rescue a civilian ship... is to destroy the civilian ship. Calhoun reasoned that either the Maru's crew was already dead, or they would be Klingon prisoners after he lost the hopeless fight, an idea to which death would be preferable.
This was likely inspired by a sequence in Star Trekker, a parody manga briefly published in the early 90's by Antarctic Press until Paramount came down like a mountain on them. In that case, the resulting explosion crippled the nearby Klingon cruisers. The (Japanese) captain was ordering a followup strike to take advantage of the Klingons' momentary confusion when Admiral Kirk himself kills the simulation and walks in to dress down the captain. She, in turn, explains succinctly that as Klingons do not take prisoners and saving the vessel was a clear impossibility, priority had to be given to saving her own ship...which Kirk dismissed, but later we see that it was really more a matter of him not wanting anyone else to win the simulation.
Miles Vorkosigan once threatened to shoot the hostage, in order to turn a hostage situation around, and make it the hostage taker's problem. note The hostage was his emperor. It really threw their opponent off balance, Gregor picked up immediately and played his part beautifully.
It's also mentioned that, in a world with stunners, this is a really good option - stun everyone (hostage and hostage taker alike) and sort them out once they're unconscious. It wasn't an option in the case above because the hostage taker had Power Armor.
Artemis Fowlonce had Butler shoot his own father in order to trick the Russian Mafiya. Of course, it wasn't a real bullet — it was a fairy capsule designed to hold water rations, filled with his own blood. Unfortunately, the mafiya ended up throwing the man into the Arctic water anyways...
In Exile's Honor, Alberich is training battle/bodyguards for then-Princess Selenay, and knows that she's more likely to be taken hostage than just killed. We don't get to see that session, but he fully intends to teach the guards to shoot Selenay in the leg if this happens, because it will slow down her captors. (Being an intelligent man, he plans to save that lesson for a time when Selenay is not present.)
The Tie-In NovelMonk novel Mr. Monk and the Blue Flu has one. The temperemental detective Mad Jack Wyatt threatens to shoot through Monk after Charlie Herrin tries to use Monk as a human shield. Afterwards, Monk congratulates him on his "bluff", but he wasn't bluffing — he always shoots the hostage.
In the first novel of The Dark Tower series, The Gunslinger, Sheb uses Roland's lover, Allie as a shield and hostage. Roland kills her out of pure instinct; his trained hands react quicker than his mind. Changed in the revised edition.
In The Han Solo Trilogy, Han attracts the attention of local authorities on Coruscant when trying to access a bank account that had been flagged. He takes a bank manager hostage in order to escape. The Stormtroopers' response? Shoot the bank manager.
In the Saga Of The Noble Dead book The Dog in the Dark, Leesil does this to save Captain Bassett. Since it's a high fantasy world, he does it with a thrown stiletto rather than a gun, but the principle is the same.
In Legend of the Five Rings, a Scorpion Clan woman did it too. After seducing a Crane Clan bushi to let her into the castle where her children were held (against his explicit orders), she killed her own children, pointed out she not only could have more kids, but was was pregnant with his child... So he committed seppuku.
Darreon in Lucky Dawg tries to taunt the 4 Horsemen Of Alliance with a Sadistic Choice - he will kill a little girl, unless one of them will take her place. However, the 4 Horsemen, being assholes, just kill his hostage. Too bad for them, Darreon was looking for a hero to fight, not somebody like them, so he slaughters them in very brutal way.
In Flip Side, when a knight Bernadette humiliated by kicking his ass in front of the knight council gets ahold of the magic crazy-making super-power-giving collar-outfit-thing and goes after her in a bar, and then tries to use her as a human shield when Maytag shows up, Maytag makes it very, very clear that she will kill Bernadette herself rather then allow Bernadette to be raped and murdered. And, despite the fact one of her main skills is bluffing, Maytag is perfectly serious. Luckily, she wins.
In the Beast Wars episode "The Low Road". Of course, they all heal injuries regularly, and the hostage in question is a Reliable Traitorat best.
Dinobot: (holding Tarantulas) Do not fire, Megatron! I have a hostage! Megatron: Why, so you do. *Fires*
Code Lyoko featured a situation where the team leader, Jeremie, ordered Odd to shoot a teammate to force XANA to free her from mind control. Considering that teammate was Aelita, who's both Jeremie's best friend and his love interest, this took some serious guts.
Then again, Aelita would have died if they hadn't threatened to kill her, so this becomes a bit of Taking You with Me, rather than sheer guts.
Real-life law enforcement often uses non-lethal weapons in hostage situations for this very reason, amongst others.
During the Beslan school hostage crisis involving 1,200+ hostages (including over 700 children), one of the children managed to slip out a window, but was so traumatized and disoriented by the ordeal that she ended up wandering around into everyone's line of fire. According to a Military Channel documentary on the Russian Spetsnaz commandos, some of the commandos seriously considered shooting the girl in the leg in order to keep her still and prevent her from being killed outright by the increasingly erratic and panicky hostage-takers, who had already executed numerous hostages.
According to some accounts, as many as 80% of the hostages who died were not executed by the terrorists but were killed by indiscriminate fire (including with heavy weapons like tanks and rocket launchers) from the Russian military, who were widely accused of not caring about rescuing anybody, just about killing the terrorists.
Most prisons will politely inform visitors that they have a 'no hostage' policy. Whether this extends to simply not negotiating for your release or full on not caring if you're the human shield is never really detailed.
Some prisons, especially high-security ones, in the event of a riot or breakout attempt, typically state that guards are expendable in these circumstances. If it's a choice between shooting through the guard and letting the prisoner escape, they'll shoot through the guard. Other prisons work to avoid the trope by making sure the grounds are covered from at least two angles such that covering one opens you to another.
In certain high security areas in the military, the guards have the standing order:
"There is no such thing as a hostage, only a shield you will shoot through. If you are taken captive, you will notify the guard before you pass him."
In 1920s China, a British submarine captain was faced with the dilemma of letting a hijacked river steamer escape, or allowing the pirates to kill their hostages. He opted to sink the ship.