In The Dark Knight Returns, Batman solves a hostage situation by threatening to do this. It probably helped that the thug was new meat who didn't know about Bats' "no killing" rule.
In the first issue of The Savage Dragon, the hero is taking down a group of hostage takers, only for someone else to shoot the lead criminal: the vigilante known as Star.
The Punisher has little difficulty shooting people with human shields in the head.
In chapter seven of Bait and Switch Eleya has her away team's sniper, Lieutenant J.G. K'lak, set up on a hilltop with a vantage point over most of the village. A few minutes later she announces herself to a group of Orion Syndicate mooks and orders them to surrender. One of them grabs a 14-year-old girl and threatens to kill her, whereupon Eleya barks, "K'lak, take him!" into her combadge and the Klingon headshots the mook from behind.
In The Fifth Element: After Korban takes out a few of his men, the lead Mangalore holds priest Cornelius hostage and threatens "One more shot, we start killing hostages! Send someone in to negotiate!" Korben's method of "negotiating" is to calmly walk in, Boom, Headshot the leader, then ask "anyone else want to negotiate?" while waving his gun around at the rest.
The Matrix Reloaded: While fighting one of the Merovingian's albino ghost twins, Trinity is captured and held while being threatened with a straight razor. The albino orders Morpheus to Put Down Your Sword And Step Away. Morpheus shoots him in the head, which forces him to desolidify long enough for Trinity to escape.
In the first part of Dredd, Judge Dredd is faced with a fugitive holding a gun to a woman's head; he shoots a hot-shot into the perp's mouth, making his head burn up from the inside.
In The Fugitive, there's a sequence where Marshal Gerard and his men track down one of the other fugitives from the train crash, who takes one of Gerard's men hostage. Gerard shoots him at close range, leaving his subordinate temporarily deaf from the gunshot but still alive.
Played with in Copycat (starring Leo de Cap). M.J. shows off the Chekhov's Skill early in the film: shoot the hostage taker in the right place on his shoulder, the nerves go haywire, and they automatically drop the gun. Later, when she doesn't aim right, she's more or less directly responsible for her co-worker's death.
In Iron Man 1, Tony raids an Afghan warlord to destroy the Jericho missiles that were illegally sold to him. A group of mooks grab a bunch of civilians and start yelling something at him in whatever language is used in the area (the gist is probably "drop your weapons or we start killing hostages"). Tony targets their heads with shoulder-mounted micromissiles and blows them all away at once, leaving the hostages unharmed.
Gangster: Me and the bookkeeper are walking out of here, getting into a car, and driving away. Or else he dies. He dies, and you ain't got nothing. You've got five seconds to make up your minds. Eliot Ness:(ignores the gangster, addresses Stone) You got him? Stone:(Stone is lying flat on his back, supporting a baby with one hand and holding a revolver in the other.) Yeah, I got him. Gangster: One! Ness: Take him. Stone:(headshot) Two.
The second installment of The Elite Squad series shows this in the very beginning. During the raid in the Bangu prison, Fraga (the human rights negotiator) joins the rebel prisoners and voluntarily stands at gunpoint under Beirada's mercy just as the BOPE arrives. He begs for a ceasefire in order to avoid more killing. Officer Mathias lowers his gun and orders Beirada to drop his, and he obeys - only to get shot a split-second later. Much to Fraga's dismay and criticism of the left-wing media.
In the prologue of Last Call by Tim Powers, the Big Bad uses his young son as a human shield when his wife threatens to shoot him, and finds out the hard way that holding a small child so that his head and chest are covered leaves his groin exposed.
Forms a Crowning Moment Of Awesome in The Alloy of Law, when Lord Waxillium Ladrian has to shoot the bad guy who is holding a gun to the head of his not-a-girlfriend. However, the villain is koloss-blooded, which means that only a perfect headsot will drop him before he can pull the trigger. Furthermore, he knows this and is holding the girl directly between his head and Wax's gun. Wax's solution? Shoot a bullet off to the side and then shoot the first bullet with a second bullet in midair, causing the bullet to curve around the girl's head and drop the villain.
The stakes are rendered somewhat higher by the way this trope had been horribly subverted in the Prologue, when Wax's attempt at this had ended up killing his girlfriend after the hostage taker moved as right as he fired.
In the Law & Order: Special Victims Unit episode "Debt", the police raid a brothel run by a Chinese gang. In one of the rooms, a gang member takes one of the prostitutes hostage and uses her as as a Human Shield. The prostitute is saved when Detective Elliot Stabler dives through the door of the room and shoots the gang member in the head.
In the pilot of Alphas, Hicks is confronted with a villain holding Rachel hostage and ducking behind her in such a fashion that the shot was virtually impossible. The villain had prepared for this ahead of time and had planned to psych Hicks out so that he wouldn't be able to make the shot. Being as Hicks' ability essentially is perfect aim, he makes it by use of ricocheting the bullet.
Firefly. An Alliance lawman takes River hostage at gunpoint and gets out about half a sentence of demands before Mal storms in and shoots him in the face.
He doesn't even break stride while doing it, emphasizing what a badass he is.
In the Justified episode The Life Inside, a criminal takes a pregnant woman hostage.
Raylan: Jess, you ever hear about a spot snipers call the apricot? It's where the brain stem meets the spine. Hit a fella there, he ain't gonna pull no trigger. It's just, lights out. Jess: Oh, what, you're telling me you're that good? Raylan: Me? (He shakes his head and gestures to Deputy Tim Gutterson, beside him.) Jess: Really? Okay, this is how this is going to go down— (Tim takes the shot, perfectly.)
In Stargate Atlantis, Kolya has Weir as a hostage and is trying to drag her through the Stargate, betting Sheppard won't risk it. Sheppard calmly puts one in his shoulder and sends him through the gate without Weir.
There is a show dedicated to snipers that discusses this. Can't recall the name, but they show off various military world record holders for distance shots and at one point showcased a police officer who made a near-impossible to replicate shot against a robber who took a woman hostage in New York. A simulation (with paint-filled waterballoons strapped to moving dummies) was set up and every single sniper-in-training failed to shoot the hostage-taker (red paint) without also killing the hostage (white paint). Then they got the sniper who made the original shot (now retired) to come to the range. He made the shot.
Late in 24 Day 8, Jack needs to recover some information from Dana Walsh only to discover her being held hostage by one of the villain's main goons. The guy attempts to say "You're not gonna take the shot", but before he's even finished saying this, Jack shoots him in the head.
The bonus level "Mile High Club" in Call of Duty 4: Modern Warfare ends with you having to shoot a terrorist using a hostage as a Human Shield. On higher difficulties, you must get a headshot or you fail the mission.
In Deus Ex: Human Revolution, at the end of the first mission, you must attempt to save Josie Thorpe from Zeke Sanders, who has taken her as a hostage. Among the many options is to shoot Zeke before he can hurt his hostage.
Batman: Arkham Asylum has a non-lethal version: When Zsasz is holding a knife to Dr. Young's throat, you save her by knocking him out with a Batarang.
In Batman: Arkham City, Ra's Al Ghul holds his own daughter, Talia, hostage at knife point when Batman refuses to kill Ra's and take Ra's place as leader of the League of Assassins. Batman saves Talia be hitting Ra's with a Batarang.
Mass Effect 1 features a mission on the Citadel where some mooks take hostages in a medical bay. In a cutscene, Garrus takes out the mook holding a hostage, and after combat ends, the player, as Commander Shepard, can choose how to respond to this. Renegade Shepard's response is to compliment Garrus for taking the mook out; Paragon Shepard chastises Garrus for doing something that could have gotten the hostage killed.
This is an option to resolve the hostage crisis at the end of Thane's loyalty mission in Mass Effect 2. You can shoot his son Kolyat, the hostage taker, nonfatally, or Shoot the Hostage. The third option is a Paragon interrupt that has Shepard shoot a lamp behind Kolyat to startle him, whereupon Shepard moves in and decks him.
In "Lair of the Shadow Broker", Tela Vasir takes a civilian hostage with a similar set of options for resolving it. Among them is to have Shepard distract her while Liara throws a gorram table at her head.
Dragon Age II gives Rogue PCs a lower-tech version during the Wayward Son quest.
In Grand Theft Auto IV, Roman gets kidnapped and you must rescue him; you finally find him used as a hostage by a Russian mobster. You must carefully aim for the Russian's head to free him.
In Army Of Two: The 40th Day, enemies will sometimes use civilians as human shields. You can do this to them, but if you're not careful, it's possible to kill the enemy and the civilian with the same bullet. Also, your partner can rescue you this way if an enemy holds you hostage.
This is the usual way for Cole Phelps to resolve a hostage situation in L.A. Noire. Don't take too long to line up a shot or you'll lose.
The second boss of the first game uses an old woman as a human shield, but an able player can off the boss without hurting the woman (who will then wave happily at the player.) Just wait for the boss to pop out to shoot you, and blast him then.
The sequel, Operation Thunderbolt, does this in the final stage, where you confront the lead hijacker on the plane and he uses the pilot as a human shield. Kill the pilot and you get the bad ending; wait till the hijacker pops out to shoot you and blast him till he goes down to get the good ending.
S.T.A.L.K.E.R.: Call of Pripyat has one particular side quest in the second map that has you rescuing a captive stalker from a gang of bandits in a holed up warehouse, due to a deal gone wrong according to his friends. You can choose to storm the place either by yourself or with the stalker's known friends and launch the daring rescue. Once you get to the last room in the warehouse, the bandit ringleader has a gun pointed behind the hostage and warns you to not make any sudden moves. At this point, you have the golden opportunity to make a carefully placed head shot on the ringleader; however, you have only three seconds to do it before he pulls the trigger and effectively shoots the hostage dead (and thus failing the quest).
In the first half of Stage 3-3 of Time Crisis 2, Ernesto Diaz uses Christy Ryan as a hostage shield. The players have to engage Diaz accurately, otherwise, a missed shot hitting Christy will cost 5000 points.