Many villains are ruthless and uncaring about the world around them, perfectly willing to hurt innocents to further their gains, but it's not always this way. Sometimes, you'll run across a villain who, while just as greedy and self-serving, still makes sure not to hurt those around him, and is not willing to kill and destroy innocent lives just to get ahead. Offer them infinite power if they'd just kill a single innocent, and expect them to say no; of course, that doesn't mean they won't accept the infinite power if they could get around the whole "killing the innocent" part. These villains are some of the more human villains out there.
Generally, this is shown as villains trying to avoid harming people who aren't involved, and making sure not to kill innocent people. Unfortunately for our heroes, they don't count, so they can expect every weapon at these villains' disposal to be aimed at them.
This is a must for the Hitman with a Heart an Anti-Villain, Noble Demon, or Anti-Hero, a form of Even Evil Has Standards, and is a Sub-Trope of sorts of Affably Evil. See also A Lighter Shade of Grey, when something like this makes them look good despite a total willingness to kill the guilty, and Punch Clock Villain, for villains who take this to the next level, and only act villainous because it pays the bills (though it's not a given that they'll be like this). A Blood Knight may also exhibit this, although in their case it may be more down to innocents never putting up a good fight. Don't expect Omnicidal Maniac and Psycho for Hire to adhere to this trope.
Some subtropes denote specific groups or classes of persons as off-limits:
In Hunter × Hunter, Zeno Zoldyck is a ruthless assassin and has killed thousands of people in contracts over decades, but is completely unnerved when one of his stronger attacks ends up mortally wounding a civilian in the area and forfeits the job, mentioning he just killed someone unrelated to the job for the first time and is visibly upset.
Light in Death Note thinks of himself as this; his stated intention is to kill all the criminals in the world to make it safe for innocents. But he's really bad at that in practice. As soon as he hears that L plans to stop him, he shifts right into "all who oppose me must die" mode.
He manages it alright during the Yotsuba Arc, where it's shown (as if we weren't already aware) that his morals when he doesn't own a Death Note are an almost direct lift from his father — which brings them both into conflict with L.
Mahou Sensei Negima!: Just about every major villain to appear generally falls into this. Chao took great pains to see that no one would be injured, and Negi is the only person that she actually fought seriously against. Later on, Fate has stated that he has no desire to hurt anyone except those who are actively opposing his plans, and that the only person he actually wants to kill is Nodoka, as her Telepathy makes her too dangerous to his plan. It's actually a bit of a Double Subversion, as his ultimate plan seems to be erasing the magic world from existence, but he thinks that he's doing everybody a favor.
Even the demons summoned in the Kyoto arc (not counting the Demon God); when they just think they're being sicced on "ordinary teenage girls" assure Asuka and Setsuna that they'll just beat them up; not kill them or anything.
The two anti-villains of Fullmetal Alchemist, Greed and Scar fit this. Greed is greedy for followers, so he has no interest in harming innocents. Eventually, he actually tries to save people. This is a sharp contrast to the rest of his siblings. Scar starts off as a Serial Killer targeting only State Alchemists, generally those who fought in and committed genocide during the Ishvallan War, although he also tries to kill the protagonist.
Kanone in Spiral has a strict rule to only kill Blade Children. This is something that is used by Ayumu to help defeat him. Kanone has amazing reflexes, but he always makes himself pause for a moment to ensure he is not killing a normal human rather than Blade Children. So Ayumu takes advantage of that.
While Tiger & Bunny's Lunatic will kill criminals and attack people who aid criminals (like, say, heroes trying to prevent his assassinations), he won't hurt someone he sees as innocent according to his moral code. So when he realizes that Kotetsu has been Unpersoned and framed for murder, he's the first to help him out.
A Certain Magical Index: Accelerator, for all his sadism in combat, holds the attitude that innocents should be left out of the conflicts of "the dark side" of the world. His definition of "innocent" is pretty narrow, though. Attack him, however ineffectively, or just be involved in shady dealings, and you deserve whatever's coming to you, as far as he's concerned.
In YuYu Hakusho, Toguro (the younger one) mostly will not harm innocent humans or demons unless either they go against his master plan, they are contract kills, or they are fighting against him in a competition. But that's only if he's in his more human forms. If he's at more than even 70% power (meaning 70% demon), all bets are off, evidenced by his willingness (almost eagerness) beginning at 85% power to vacuum the souls of apparitions in the bleachers of the Dark Tournament to feed his power even further.
Toguro (Human Form): "I only kill true fighters and job assignments. And you are neither. So run along."
X-Men: Depending on the Writer, Magneto can be one of these. It's generally a given that he won't take a mutant life if he can help it, and, if he's one of his less megalomaniacal moods, will avoid attacking humans that aren't his targets or against him (in his other moods, all humans are his targets).
The Flash's Rogues Gallery is generally made up of people who probably wouldn't make a plan around shooting an old lady crossing the street. Explicitly stated a few times as something of a survival strategy. They really don't expect superheroes to intentionally kill them, but they know being homicidal maniacs will bring more than just the (usually rather reasonable, and sometimes even friendly) Flash down upon them. Many of them are also probably self aware enough to know that their issues combined with killing needlessly would probably land them somewhere like Arkham, and they know they don't want to be cooped up with the kind of people that wind up there.
Depending on the Writer, this can be the case with Harley Quinn. During her solo series, she never killed cops, guards, superheroes or bystanders, usually leaving them knocked out or Bound and Gagged instead. When she did kill someone, it was usually made clear they were a "bad" person. Other stories, however, do show her taking innocent lives (or at least endangering them), usually at the behest of The Joker.
Deadpool criticizes a group of mercenaries who saved him from jail by killing everyone who was guarding him. When they insist it doesn't matter because they're just cops, Deadpool snaps back that they were only trying to protect their people (the town was currently infested with zombies... long story). And then he kills them all and goes on alone.
The Hulk is like this. He may rage to high heaven and destroy an entire city, but he has never killed anyone deliberately... or even accidentally! Best not to think about the latter too much. Ultimate Hulk is, quite graphically, as far from this as you can get. Then came the "Heart of the Monster" story arc in Incredible Hulks when he wound up in the Dark Dimension. Where no one is innocent. And his ex-wife and his worst enemies were there too.
Venom from Spider-Man, Depending on the Writer. Even during those times, though, even if he'd never hurt anyone he decided was innocent, it's hard to know who will or won't fit the criteria (due to his being Ax-Crazy, if less so than Carnage.)
The Teen Titans foe Cheshire started off like this. One Action Comics story had her assuring a Bound and Gagged hostage that she had no intention of harming him, since she just needed him out of the way for a little bit in order to kill her real target.
In the MAX series at least, this is one of the reasons The Punisher is an AntiHero. He takes great pains to avoid civilian casualties while he's gunning down dozens of Mooks, and at one point he nearly kills himself because he thinks he shot an innocent. note The innocent was already dead, and the situation was set up so that he would think he killed her. Castle only realizes this when he exhumes the corpse and compares the bullet wound to his weapon. The mainstream Punisher, depending on who's writing him, is portrayed as trying to not kill innocent civilians or the superheroes who try to stop him. Of course, other writers have had him attempting to gun down jaywalkers. And he did kill off his sidekick's girlfriend while brainwashed, though at an earlier time, being ordered to kill Spider-Man (an innocent) broke the brainwashing a different villain subjected him to.note In one of his earliest appearances, it's said that he had vowed to turn himself in if he ever killed an innocent. In the final story arch of his original series, he nearly goes through with it too after accidentally gunning down a family (it was later retconned that he wasn't the one who killed.)
Demogoblin; a demonically possessed variant of the Green Goblin/Hobgoblin/etc. from the Spiderman universe was out to kill all sinners in the world. His final death was saving a mother and child from a collapsing church.
Skurge the Executioner fought on the side of evil in an effort to win the love of Amora the Enchantress. However, he was brave and noble, and never attacks anyone besides his target. In one story, Thor realized the Skurge he was fighting was an imposter because the fake slapped a child in his path.
In The Super Hero Squad Show, he surrenders when he accidentally knocks a frozen solid Valkyrie off a building, where she would have shattered if Thor hadn't caught her.
Skurge: (while using a heat blast to defrost Valkyrie) "My mad love for Amora almost cost an innocent's life!"
Ken, Ray and Harry from In Bruges are very specific about never killing anyone who is innocent (particularly notable with Harry since he is otherwise quite sociopathic). At one point, Harry is very careful not to shoot in a crowded area, and both he and Ray adamantly refuse to fight with a pregnant woman standing between them. When Harry believes himself to have accidentally murdered a child at the end, he immediately commits suicide because he considers what he has done to be unforgivable.
They mostly adhere to this. Given their profession, it's more like never hurt an innocent without a "good" reason. Children are the main way it's played completely straight - while the story is the result of Ray accidentally killing a child, and Harry commits suicide because he thinks he did, the child Ray killed was behind his target, a priest who just got in the way of Harry's business. Ray does assume he was following this fairly closely until he finds out about that, though.
Inside Man: The robber running the bank job will not hurt anyone who doesn't force him to do so, kills no one, and is actually trying to bring down someone who did kill many innocents.
John Q.: The only thing the main character cares about is his son, and has no intention of killing anyone.
In Jumanji, Egomaniac Hunter Van Pelt is summoned by the game to hunt Alan, who rolled him up — but, as it turns out, only Alan. Van Pelt can't or won't directly harm anyone else (and lampshades this), though he has no compunctions on collateral damage in the process of slowing Alan down, as long as nobody else gets anything worse than an inconvenience.
Predator: The Predator species generally avoids killing unarmed opponents, since they considered it poor sport. This also includes weak prey such as pregnant women and cancer-afflicted humans. Only when they actively pose a threat anyway do the Predators consider them fair game.
Leon, The Professional, has very simple rules about his clients: "No women, no kids, that's the rules."
The Rock: Francis Hummel he takes innocents hostage and threatens to launch a chemical strike at San Fransisco, but he refuses to harm any of his prisoners and deliberately sabotages his own missile launch to avoid civilian casualties. And just before he takes over Alcatraz, he has a bunch of kids on a field trip and their teacher get out of the complex.
Scarface (1983): One of Tony Montanna's good traits. He blew the brains out of an assassin he was supposed to drive around because he was willing to kill the targets wife and children just to get him.
In Terminator 2: Judgment Day John Connor tries to get the T-800 to do this by asking him not to kill anyone. The terminator complies by shooting a security guard in the knees. When John protests the terminator coldly responds "He'll live."
In the X-Men films, as above, Magneto is usually like this. In the 3rd film a family are trapped in their car when the bridge is moved, and once it is moved, Magneto notices them, frowning in surprise. The mother locks the door and he turns away smiling. He also seems not to toss that particular car, and with a couple of notable exceptions (Rogue and possibly the policemen guarding Mystique), most of the people he kills are cases of Jerkass Victim (e.g. the security guard and Stryker). The exception is attempting to turn Stryker's plan in X2 around to kill all non-mutants, though that was more impersonal.
Since the Jedi in Star Wars are peacekeepers this is a natural rule for them. They have respect and compassion for all life and frown upon hurting the innocent unlike their counterparts the sith
Silent Night, Deadly Night: Billy goes on a rampage to punish those who are naughty, while leaving those who are deemed nice alone.
In The Star Chamber, Hardin refuses to see two men die who are innocent of murder, although they're possibly guilty of others (it's shown they have committed serious crimes, though murder is not shown to be one.) Caulfield, on the other hand, argues they can't risk exposing themselves and have to pursue the greater good-plus as stated the criminals were guilty of something, in an impromptu debate on morality.
Artemis Fowl: When Artemis is accused of being just as bad as the current villain, he uses this trope as a defense.
Commander Thrawn tries not to kill anyone who isn't his enemy. He'll fire at Vagaari ships, which have Living Shields, saying that they are already dead; if the Vagaari's tactics don't kill them in this battle they will die in the next, and stopping the Vagaari now will save more people in the long run, but he's unhappy about doing this, and makes plans to avoid it in the next engagement. This may be an extension of his species' brand of Martial Pacifism, although Thrawn himself ignores their rules whenever they're inconvenient. He is deeply, deeply unhappy about what happened to the fifty thousand innocents on Outbound Flight.
In Outbound Flight he's about as non-evil as Thrawn gets. In later-set novels, while his plans and tactics show him to be A Lighter Shade of Grey and he avoids killing innocents when possible, he's very much more pragmatic.
The stormtroopers who later formed the Hand of Judgment got in trouble with the Imperial Security Bureau because at least one of them refused to shoot unarmed civilians, never mind that they were supposedly Rebels. This lead to him semi-accidentally killing the ISB officer who confronted him with a blaster, which led to him and his friends deserting. That same stormtrooper, LaRone, who aimed to miss ended up being the leader of the group; another of them explains how, ending with the fact that refusing to kill innocents gives him the moral high ground. Confused, LaRone says that he thought all of them did that, and he is told "I obeyed orders."
The Dresden Files: One of the things that makes "Gentleman" Johnny Marcone a Noble Demon (despite being The Don of Chicago) is the fact that he goes out of the way to ensure children never suffer the ill effects of his "business". If someone in his organization hurts or sells drugs to a child, God help them.
Going Postal: This is something Moist von Lipwig prides himself on. Subverted when Pump 19 tells him that Moist's cons and scams, while not hurting anyone directly, have caused harm equivalent to the murder of 2.338 people. This is brought home when he learns that a previous job of his working to defraud banks working with bonds and letters-of-rights made his love interest lose her job.
In the TV adaptation, the number of people Moist "killed" increases to 22.8 and his fraud causes the bankruptcy of his love interest's family (and gave the book's Big Bad the opening he needed).
The members of the Assassins Guild could be argued to fit this trope. They would never kill (or ‘inhume’ as they call it) someone unless they are paid to do so and the victim (client) must have a sporting chance. They won’t take out a contract on someone who can’t defend themselves but if you can afford a bodyguard then you’re automatically deemed able to do so. They prefer to inhume their clients at their place of work or at home rather than the street. Although it’s accepted for them to inhume a client’s bodyguard or another assassin while performing their service, they wouldn't dream of killing an innocent maid who just happened to be in the house at the time. They are polite, efficient and will even clean up afterwards.
Live Action TV
Dexter: Dexter makes a point of only killing other serial killers. Even apart from the Code of Harry forbidding him to harm innocent people, he's disgusted by the idea that anyone could harm children, though for the most part he kills other murderers because it causes less trouble with the authorites when they go missing or turn up dead that out of any true condemnation of their activities, though that does occur on occasion.
Sylar in Heroes has made it clear that he doesn't just kill people for fun - only if he needs their powers. On the other hand he has also made it very clear that he does enjoy killing people - even continuing to mutilate his victims after figuring out how to replicate their powers without doing so and commentating that he almost forgot what fun it was. Apparently the thrill of it is not enough to go after ordinary, and therefore useless, people though.
In season 1, when Sylar first comes to the (incorrect) realization that he is the bomb that will blow up New York and kill half the population, he goes through utter turmoil, asking Mohinder for help. According to him, he only kills because he sees it as an evolutionary imperative that he acquires new powers. He only kills evolved humans who have powers he wants. He does not want to kill 4 million regular humans. He eventually gets over it after (inadvertently) killing his mother.
From The Wire, Omar Little, Badass Extraordinare, has a code of honour that means not hurting anyone who isn't in the Game. No doubt.
Boss Hogg in The Dukes of Hazzard never hurts innocent people. The actor who portrayed him in the series only agreed on the condition the character wouldn't do certain things. Hurting innocents was the most known item on the list.
In the Doctor Who episode "A Town Called Mercy" The Doctor finds a town beseiged by a cyborg gunslinger who keeps supplies from arriving and demands one occupant. When confronted by The Doctor, the cyborg confesses his strategy is to prevent others from getting in the way. Eventually, however, the gunslinger concedes that he needs to take a more direct approach which he re-evaluates on realising he is pointing his Arm Cannon at a child. He leaves the town without harming anyone.
The Sarah Connor Chronicles: Cameron, being a good robot, is expected to avoid hurting innocents (although her definition of a non-innocent is sometimes called into question). However in one episode a bad robot is attempting to "kill" Cameron, and the fight continues in an elevator, but suddenly both combatants — including the bad robot - suspend their battle when an innocent bystander briefly boards the elevator. Possibly that had more to do with preserving the Masquerade than anything else, at least on the other Terminator's part.
This is one of the main tenets of the Assassin's Creed. Altair's disregard for innocent lives and arrogance lead to him being stripped of his rank within the Assassin Brotherhood. In-game, harming civilians will cause the player to desync since none of the playable assassins killed civilians. Averted however with Shay Patrick Cormac of Assassin's Creed: Rogue, who as an Assassin turned Templar has no such compunctions.
Hitman: It varies. While Agent 47 is very much into Pay Evil unto Evil, he only cares about his contract, and will kill innocent people if he's paid to. That said, for the sake of professionalism and avoiding unwanted attention 47 canonically avoids killing civilians and at most will simply knock them out.
In Mass Effect 2, Justicar Samara's code prevents her from ever hurting an innocent person, even if she must allow a criminal to escape in order to prevent it. Apparently, this tenet of her code is overridden if that innocent person poses any threat to the Justicar herself or attempts to impede her investigations, though Samara is willing to exploit loopholes in her code to take alternate options when she can.
In The Godfather: The Game, while you can freely indulge in Videogame Cruelty Potential while free-roaming, some missions ask you not to kill innocents. Inverted in one contract hit, where you need to ensure there are no witnesses for the Respect and monetary bonuses - guess what?
In Scarface: The World is Yours, Tony says that he cannot hurt civilians when he attempts to shoot one. However, he can still punch them and run them over with a car.
Thief: Garret may be a thief and an outlaw, but he does not look kindly on harming innocents. Oh, the player may still do it, but it's considered a bad mark by the game.
In Borderlands 2, Krieg's personalities have a simple agreement: the psycho side of Krieg can kill as many evil men and savage beasts as he wants, so long as he stays his wrath from the innocent. If the murderous side does harm an innocent, the moral half of his mind will take control and force them to immediately commit suicide.
In the inn scene of The Order of the Stick, the assassins who are after the king of Nowhere try to avoid hurting anyone who is not involved. Too bad they think that Roy is the king of Nowhere, due to Who's on First? problems.
In Schlock Mercenary, Tagon is faced with the choices of revealing the Gatekeepers are copying people using wormhole gates and then interrogating the copies, killing the copied people once the interrogation is finished and starting a war that would lead to the end of galactic civilization, or remain silent and let the gate clones continue to be killed, both of which result in massive loss of innocent lives.note Admiral Breya suggests a third option, when Tagon discusses the choices with her.
Dr. Horrible of Dr. Horrible's Sing-Along Blog is this way, at least at first. He refuses to fight a hero in a park because children play there (well, that and he doesn't have time to fight every "poser in a parka"). He also tells a room full of civilians to flee before he tries to off the hero, Captain Hammer. Plus the fact that he never really crosses over the Moral Event Horizon completely shows that, even after getting a seat on the Evil League of Evil, he still has problems with truly hurting innocents.
My Little Pony: Friendship Is Magic: A non-villainous example appears in "Griffon the Brush Off". Pinkie Pie and Rainbow Dash have a fun day pulling practical jokes on their friends in Ponyville, except for Fluttershy, whom they leave undisturbed because she's too innocent and sensitive for their pranks.
Sandman in The Spectacular Spider-Man was never truly malevolent, he was just in the villainy game for the money, and hoped having powers would finally get him the "big score" he always wanted. In episode 18, he helped save the passengers of a ship about to explode. A ship he was trying to rob until his fight with Spidey started a fire.
Spider-Man: Sandman, stop! You... [watches Sandman place the crewmen he'd grabbed into the life rafts] ...saved them?
Sandman: I was just in it for the bucks. I never meant for this to happen.