"The true interest of an absolute monarch generally coincides with that of his people. Their numbers, their wealth, their order, and their security, are the best and only foundations of his real greatness; and were he totally devoid of virtue, prudence might supply its place, and would dictate the same rule of conduct."
— Edward Gibbon, The Decline and Fall of the Roman Empire, Chapter V
In Code Geass, Cornelia tries to fight the drug trade because the drugs hurt productivity among the conquered Japanese.
Dutch from Black Lagoon runs illegal booze, slaves, guns and drugs. He does piracy when the delivery business goes slow. He does not, however, condone his employees running off Ax Crazy and taking out their issues by shooting at noncombatants when he's in a combat zone. Not because he gives a crap about their lives, but because he wants to know that his backup can be relied upon and stay professional.
Most of the cast of Black Lagoon act out of this trope almost all of the time: People who don't seldom last long (except Revy, who has a tendency to run off Ax Crazy when she has a bad day but is also a main character). Balalaika averts it once when she declares personal war on Hansel and Gretel for killing one of her men, though she also had a pragmatic reason since the pair were destabilising Roanapur by their presence.
Dutch also says in the manga that he doesn’t want to risk himself in an operation that could make him a lot of money, (dooming himself to work for significantly less money that other operators) because he knows doing the job is a great way to get himself killed).
The Gandor Family in Baccano stays steadfastly out of the drug trade, sticking with relatively less objectionable crimes like bootlegging and gambling. This is due to actual moral objections on the part of Keith Gandor, but the other two Gandor brothers, Luck especially, recognize that it's also because their relatively small organization is not equipped to compete with the larger organized crime families currently running drugs.
The Maou in the light novel/manga, Maoyuu Maou Yuusha is an example of this, although she is more pragmatic than evil.
Moo in the Monster Rancher anime captured Holly to use the Magic Stone to locate his original body, figuring he could destroy the heroes with it. They rescued her, but by that time he had gotten what he needed to know. Rather than let them find out where he was going or try and stop him in his humanoid form, he simply left them behind so they had no idea where he was.
Seeing as how Vegeta is eventually defeated, and won over (more or less) to the side of Earth, the fact that he ends up marrying a human and having a child with her suggests he's at least possibly implementing the interbreeding plan with the aim of now protecting his newfound home.
This is the reason why Ginjo from Bleach told Tsukishima to stop Mind Raping Chad and Orihime. He has no moral objection to it, but destroying your hostages' minds means you can't use them as pawns. It's easier to just stick to Mind Control.
Mayuri has shades of this too. He sticks with the Soul Society because it gets him: an officer position, funding, minions, supplies, etc. Working freelance gets you an execution by the Soul Society.
Kenpachi Zaraki helps save Rukia, not because he believes that her execution is morally wrong... but because he wants to fight Ichigo again. That and it gives him a rare opportunity to fight against his fellow captains, some of the strongest possible foes.
In Magical Record Lyrical Nanoha Force, Arnage and Veyron take on two other Eclipse infectees. The latter's willy-nilly attacks on innocents will be blamed on the Huckebein, who don't want the added attention.
Death Note has Villain ProtagonistLight Yagami who was willing to kill tens of thousands of criminals and other undesirables to further his ambitions. But he doesn't approve when his Bumbling Sidekick Teru Mikami, announces that Kira is going to kill lazy people as well... because Light considers the move premature. Once all the criminals are dead and Kira is regarded as God, Light fully intends to prune out other undesirable elements from "his" world.
In Naruto, it could be argued that every ninja village practices this. While glossed over, the series does admit to ninja taking jobs like kidnapping and assassination. By and large, everything a ninja village does is either to win a war or because they were hired to.
Crime Boss Wallenquist from Sin City refuses to seek revenge on Wallace, who almost singlehandedly dismantled his human slavery market, because there's no benefit to him.
"Revenge is a loser's game. There's no percentage in it. All that matters is profit and power."
The Shocker, one of Spider-Man's enemies, is almost unique among the wall-crawler's enemies in that he's rarely concerned with taking revenge on our hero and prefers to only commmit crimes that are actually profitable. Of course, superhero comics being what they are, Spider-Man is almost always the one to interfere with the Shocker's robberies.
The Hobgoblin started out with this, vowing to avoid the Green Goblin's mistakes and only went to kill Spiderman to make sure he wouldn't mess with his plans. However, these traits were lost.
He needed Wonder Woman to point it out, but no, Ares does not support nuclear and biological war. If everyone died, there would be no one left to fight wars anymore.
Darkseid will never try to conquer the universe through Time Travel on the grounds that it is far too reckless. There are simply far too many things that could go wrong when you alter history.
He objects to Desaad and Sleez's acts of evil because they are largely pointless. Desaad is a petty sadist. Sleez once mind-controlled Superman, but instead of doing anything useful with him like trying to conquer the world, he made Superman star in a porno.
Another example occurred in Cosmic Odyssey (not surprising, since Odyssey had basically the same plot as Crisis on Infinite Earths), in which it was Darkseid, of all people, who organized the heroes to fight the Anti-Life Entity. Of course, Darkseid did try to manipulate the situation to his own advantage, fully in keeping with this trope.
Christu Bulat from The Punisher MAX, in total contrast to his father. The relationship between the two is rather strained because Christu views human trafficking as a business and raping girls as just part of the business. He also berates his father for using his bare hands instead of a gun to kill a gang member, as well as for shooting the whole gang. As you could guess from his profession, though, he's still a heartless, raping bastard.
His pragmatism is best demonstrated by his willingness to kill his own father. It doesn't work out, both because he underestimated his father and because he gets disemboweled.
In the Watchmen universe, after the "costumed hero" phase hit its peak, most costumed villains started either reforming entirely or switching to "less showy" pursuits like drug dealing and prostitution rackets.
He himself also invokes the trope, whenever the bad guys do a Villain Team Up, they RARELY (If ever) invite the Joker in. While most of them were genuinely afraid of him, some of him didn't like The Joker because he's not exactly a team player and is considered unprofessional and untrustworthy even from his fellow villains. The exception is Lex Luthor, who does invite him if he's in charge of the villain team ups on the basis that it's safer to have an unpredictable Joker on your team than it is to have an unpredictable Joker who's offended you snubbed him.
You're Dracula. The series is Requiem Chevalier Vampire. Six million lemures, the souls of those who were mistreated and murdered in life and can only be stopped by killing their tormentor in death, are swarming your ship. Do you fight them all one on one? Or do you step into your back room and break Hitler's neck, wiping out all six million in a stroke?
The Red Skull may indulge in petty wasteful sadistic villainy often, but he does not appreciate anyone on his payroll doing the same. Villainy committed on his dime has to have some kind of profit for him.
One comic showed him foiling a plan by Madam Hydra, her subordinate at the time, that wanted to blind every American who was watching a television set at some point. He said he was called a lot of things, but never a Nihilist anarchist.
Hilariously, he once renounced Nazism to embrace...nihilist anarchism. It didn't take.
In A Cure for LoveLight becomes irritated when he learns his followers have opened death camps because it's not as efficient nor as controlled as killing with the murder notebook, not to mention it's bad for P.R.
In the Pony POV Series, the Dark World version of Discord often has to reign in Fluttercruel and keep her from killing their victims, because he feels that having subjects to torment in the long run is better than killing for a thrill in the here and now.
The Villain Protagonist of Lord Of War, Ukranian-American arms dealer Yuri Orlov, at one point reveals he has never done business with Osama Bin Laden "not on any moral grounds" but because "back then he was always bouncing checks." In fact, he even shipped cargo to Afghanistan while they were fighting the Soviets. His rival, Simeon Weisz, would only sell weapons to those whom he wanted to see fulfill their goals. In the case of the Iran/Iraq War, he supplied both sides in hopes that they would both lose.
In The Ten Commandments, Moses is given charge of using slave labor to build Pharaoh's new treasure city. When he takes charge, he improves the slaves' food ration and gives them a day off to rest. When Rameses protests that he's being wasteful, Moses replies, "Cities are made of bricks. The strong make many, the weak make few, the dead make none," and then shows Pharaoh that the city is being built faster than before.
In Avatar, the mining corporation uses the Avatar program as a tool of diplomacy to try to peacefully negotiate with the natives for their land and to research the planet. The company executive points out this was done because killing an entire tribe for their land would cause public relations problems. They'll only try to wipe out the Na'vi if they have to.
The Prophecy featured a pragmatic Lucifer (played by Viggo Mortensen) who has the angelic habit of perching atop things like a bird. Satan saves the main cast from an evil Gabriel, who was on a rampage against mankind. His own selfish motives being "we don't need another hell up there".
Constantine also has Satan help foil a rogue angel's plot to help his son unleash Hell on Earth, since being Satan is his job.
In Pirates of the Caribbean: Curse of the Black Pearl, Captain Barbossa believes he needs the blood of Elizabeth Swann to remove the curse of undeath plaguing him and his crew. When he first tries the ritual, he simply takes a few drops of her blood, since that's all he thinks it would require.
Barbossa: Begun by blood...by blood undone! (nick)
Elizabeth: That's it?
Barbossa: Waste not.
In Reservoir Dogs, Mr. White and Mr. Pink disapprove of Mr. Blonde's killing spree...not because they have any qualms whatsoever about killing someone (they don't) but because they need a reason, even if that reason is "I'm fleeing the cops and you're standing in my way." Mr. Blonde appears to kill and torture For the Evulz.
Sonny in A Bronx Tale is the only one to willing to work and deal with black people for profit, while the more racist mobsters want nothing to do with them.
In Lawless, Floyd Banner saves the life of Jack and Cricket from his goons, gives them a great fee for their moonshine (whose quality he is impressed with), gives them the address to the creeps who attacked Forrest and finally whacks his mook who almost killed the boys with a shovel while roaring that he has enough trouble from the law without starting a needless feud with a local tough crime family.
In Miracle on 34th Street, Macy goes along with Kris's "send people to other stores because Macy's doesn't have it/doesn't have a good enough version of it" because it will make the store seem like a nice and friendly place, insuring greater profit. It leads to an arms race with Gimbels over who could be the "customer friendliest" store.
Another scene has a judge's campaign manager convince the judge to not declare that Santa Claus does not exist, because it will make the judge completely unelectable.
He didn't administer a reign of terror. Just the occasional light shower.
In both Going Postal and Making Money he's confronted by people trying to usurp him. Instead of cracking down on them, he points Loveable Rogue Moist Von Lipwig in their general direction, and waits until he makes sure his usurpers are publicly discredited. Then he reminds them he's the Tyrant and can, in fact, crack down on them.
In Jingo the D'regs have the same philosophy as Genghis Khan regarding their treatment of merchants. Kill merchants, or steal too much, and they don't come back. Rob them just enough and your sons can rob them too. Vimes compares it to farming.
In the Draka series, the Draka are horrified at the Holocaust. Because the death camps were a massive waste of resources.
In The Hobbit, the three trolls don't want to eat Bilbo, simply because he wasn't big enough to go through the trouble of skinning and boning him.
Quoth Niccolo Machiavelli: "The prince can always avoid hatred if he abstains from the property of his subjects and citizens and from their women". The Prince is the textbook for Pragmatic Villainy. He also advised that a Prince was better off with popular support over the nobility. The nobles only want to oppress, and the people just want to not be oppressed. Support of the people is therefore the better and easier path.
This position was also noted in his Discourses On Livy. Both The Prince and The Discourses heavily influenced Enlightenment thought on politics (although people tried to mention it as little as possible), and in particular is responsible for this gem, penned by James Madison in "Federalist No. 51":
If men were angels, no Government would be necessary. If angels were to govern men, neither external nor internal controls on Government would be necessary. In framing a Government which is to be administered by men over men, the great difficulty lies in this: you must first enable the Government to control the governed; and in the next place oblige it to control itself. A dependence on the People is, no doubt, the primary control on the Government; but experience has taught mankind the necessity of auxiliary precautions.
Federalist 51 is about checks and balances in the federal government. In other words, the whole point of checks and balances is to ensure that even if the whole government iscomposed of villains to a man, the structure of the system is such that it is in the interests of these villains to advance the public good. This is the entire theory of modern liberal democracy.
It's important to remember, however, that Machiavelli was in favor of republics, and "The Prince" was intended to be a critique of the behavior of despots, not a field guide.
Grand Admiral Thrawn will execute subordinates who failed and tried to pin the blame on others, but subordinates who failed at almost the exact same job who tried harder and took responsibility? Everyone braces for the order and the poor schlub sweats, but what happens? Promoted. It's a Career Building Blunder. Thrawn explains to Pellaeon that thisTractor Beam operator tried a novel technique when faced with something he wasn't trained for, that it might have failed but still looked valid, and if the operator can perfect this technique and teach it to others (shown to pay off in the Hand Of Thrawn duology), the Empire won't have a problem with people escaping tractor beams in this way. Pellaeon privately remarks that Thrawn's action also served to make everyone who saw it much more willing to give him their all.
In Tatooine Ghost, set a few months before the Thrawn trilogy, readers can infer that Thrawn put on stormtrooper armor and went dirtside with some of his soldiers, not telling them who he was but still making them aware that he was someone very important. A squad leader is rough while trying to get information out of someone, and when asked about it says he thought that brutal was the new doctrine. Thrawn hits the squad leader with his blaster, then asks the leader if he wants to do Thrawn any favors now, and orders him to tell the truth. The squad leader says no, and Thrawn pointedly says that someone who has been threatened is likely to give nothing more than what they need to survive. The new doctrine is efficiency.
Tarzen Tagge makes sure that the Tagge Company only builds the highest quality construction work. That way the customers have no reason to complain to law enforcement. An investigation would reveal Tarzen's smuggling operations. Eventually the legitimate business is so profitable that the smuggling becomes redundant.
For obvious reasons, when Corran Horn goes undercover as a pirate in I, Jedi, he prefers this sort of piracy, encouraging the gang to kill as few as possible to encourage cooperation in the future. While a few of the pirates are in it more For the Evulz, most of them recognize the potential of this racket and end up accepting a legitimate security contract at the end of the novel. Later, when the pirate gang has to fight its way out of a confrontation with the New Republic Navy, Corran convinces the crew's leader that they should use ion cannons to disable the Republic fighters... because some forces will have to be diverted to rescue the pilots, distracting from chasing the pirates.
"Put aside the profound biological differences that must exist between the hypothetical aliens and ourselves; imagine that we constitute an interstellar gastronomic delicacy. Why transport large numbers of us to alien restaurants? The freightage is enormous. Wouldn't it be better just to steal a few humans, sequence our amino acids or whatever else is the source of our delectability, and then just synthesize the identical food product from scratch?"
How to Succeed in Evil: Central character Edwin Windsor makes a lucrative, if frustrating, living counseling would-be supervillains to turn their efforts away from wanton destruction and towards more profitable strategies.
Cardinal Richelieu in The Three Musketeers is stated to have given up such petty things as vengeance, since they end up in the way of getting and keeping power.
Both Darken Rahl shows shades of this. In the first book, you'd expect Rahl to pull a You Have Failed Me when it turns out Richard broke through Denna's training. Hell, she certainly expect it. Instead Rahl reasons that her failure was no fault of her own, and shrugs it off. In the same scene, Richard plans to get Rahl angry enough to kill him, so that he can't use Richard's knowledge of the Book of Counted Shadows. Rahl calmly listens to Richard, then, after verifying his knowledge, shrugs, and gives him two options, amounting to, "Help me open the right box, or don't. I've got a 50-50 chance of getting it right either way, and if I end the world, no skin off my nose."
Emperor Jagang perhaps manages to be a bigger monster, but he's still smart enough to gather intelligence and listen to his advisors, especially when they're experts in magic and he's not. In Phantom, for instance, he and the Sisters of the Dark are looking for the Book of Counted Shadows. On finding what appears to be a copy, he thinks it's fake, while the Sisters insist it could be real. You might expect him to simply overrule them considering they're essentially slaves. Instead, they have a pretty civil debate about it. He also reads the warnings in spell books and heeds them. Jagang also reads lots of books and sends some of his best troops off looking to salvage ancient libraries in the hopes of finding knowledge from the wizards' war that could help him. He didn't even care terribly much when the Palace of the Prophets was destroyed, because the knowledge buried under in one of the "central sites" was much more valuable to him. When Kahlan is captured, has her mind erased, and is made invisible to almost everyone. Her captors are captured by Jagang, and they discover that the process that turned Kahlan invisible was tainted, and that random people will be able to see her. Instead of killing his prisoners who failed in their magic, he sends her out walking in the camp, naked (though with guards close by) to see who notices, thus assembling guards who can see her.
The Fellowship of Order sent spies to many of the wonders of the world to use or copy their magic. In one instance, they sent one of their top people to work in the stables just so he'd have a chance at copying a magical construct.
From Dune: "A pogrom? That's not like the Harkonnens. A pogrom is wasteful." Because of this, the Baron doesn't much like Rabban, who is just a brute, and he is more than willing to sacrifice Rabban for his smarter younger brother Feyd-Rautha. On the other hand, putting Rabban in charge for a while, then deposing him in favor of Feyd-Rautha makes the latter look much better by comparison. So putting a monster in charge is ultimately quite pragmatic.
Zig Zagged in Animorphs with Visser One, who claims she wants Earth to be conquered slowly and secretly because it's more pragmatic than Visser Three's plans of open war and genocide. In reality, she's worried that an open war could coincidentally kill two children she gave birth to through a previous human host. However, since the whole point of going after Earth was because there are enough people to give every Yeerk a host, the whole thing would have been pointless if Visser Three killed a large percentage of humans.
The government in 1984 outlaws the death penalty, preferring torture and brainwashing potential rebels into model citizens, rather than killing them immediately, and risk them becoming martyrs for the next generations rebels.However, ultimately they will disappear, long after everyone has forgotten about them.
When Joffrey acts Stupid Evil and wants to totally wipe out surrendering enemies and their families, his grandfather, the powerful and cunning Tywin, counsels him: "When your enemies defy you, you must serve them steel and fire. When they go to their knees, however, you must help them back to their feet. Elsewise no man will ever bend the knee to you." Underscoring that this is pragmatism rather than mercy is the fact that Tywin famously had no qualms utterly wiping out families that wouldn't go to their knees.
Roose Bolton is also extremely pragmatic, with his preference for a quiet land and quiet people. This leads to some annoyance with his son's open and increasingly inconvenient sadism.
Bolton gets a crowning moment of pragmatic villainy moments after his son expresses a desire to flay a noblewoman who doesn't like him and make her skin into footwear.
"How many of our grudging friends do you imagine we’d retain if the truth were known? Only Lady Barbrey, whom you would turn into a pair of boots... inferior boots. Human skin is not as tough as cowhide and will not wear as well."
Sandra Arminger of the Novels Of The Change is the voice of reason to her husband's pure sadism. His vainglory, too; there are times when she exhorts him to make a kill that he perceives as damaging to his reputation. Once her husband is dead and there's a firm peace between Portland and the other nearby nations, she becomes so bloodlessly pragmatic that she comes off as a particularly intrigue-oriented good guy.
In the Night Watch series, the Dark Others tend toward this when declining more villainous actions:
In one scene, a Dark Other manifests a cat to torture a mouse and his cohorts are disgusted with him because it would waste less energy to just kill the mouse himself, and he's distracted from his job of guarding their headquarters. To an exent, he's also considered to be acting Stupid Evil.
The Dark Other Edgar is shown not using magic to steal from a store because he wouldn't want to be caught by the other side and because since humans are the "resources" of his side, it's foolish to hurt them needlessly. Edgar also decides to do a light Charm Person on an attractive woman rather than brainwashing her, because (more or less) consensual sex is more fun than rape.
Zabulon/Zavulon, despite being an obvious Big Bad, is generally in the role of helping the Night Watch stop some apocalyptic scenario, since if they are allowed to happen, he won't have any victims. However, his help is always done to further some other, hidden scheme, and he's quite happy about massive casualties to the extent they help his side.
Best exemplified with Marcone, by the attitude of one of his subordinates when she saw Harry enter. "What must I give you to get you to leave very quickly."
In Death: Alex Ricker in Promises In Death demonstrates this in his conversation with Roarke. Alex reveals that the men who robbed his store and were found floating in the river all carved up were killed off by his father, Max Ricker. Max did this because the thieves embarrassed Alex and embarrassment is apparently unacceptable. Alex didn't have them killed and didn't want the problem handled that way, and that he doesn't do murder...because it's just not practical.
In Tony Hillerman's People of Darkness, the hit man Colton Wolf kills as few people as he can manage (aside from his assigned targets), because the fewer people that are killed, the shorter the resulting manhunt is.
This is one of the defining traits of the Lady in the Black Company novels- she's almost entirely devoid of compassion and mercy, and totally devoid of remorsely, but neither is she cruel for the sake of cruelty- everything she does is to get some kind of advantage, and her empire is designed to be stable and enduring. She's deliberately contrasted with her psychotic rival and sister Soulcatcher, who is pretty much pure chaos, and her ex-husband, the Dominator, whose empire, rather than being opressive but stable and organized was almost literal Hell on Earth.
The Queen in A Woman's Work is ruthless enough to encourage her son to wear bright royal uniforms while she wears something more subdued (because who will an assassin instinctively aim at?) but makes sure her people are educated (at government schools with an approved curriculum), employed, have a good medical system, knows many of her troops by name, and when she conquers a new territory has most of the defeated nobles property distributed among the lower classes of the conquered country and immediately starts infrastructure programs to help improve their lives. She even allows the odd dissident to make public speeches against her reign, giving her an excuse to remind the "oppressed citizens" that she's made their lives much better. And letting them to beat up the troublemaker.
The Corrupt Corporate Executive in Stephen King's The Running Man insists to Ben Richards that he didn't have his wife killed as part of a plan to recruit him as a Hunter. He makes no attempt to convince Richards that he's above such a thing, merely that it would have been a lousy plan and Richards would have seen through it, as evidenced by the fact that his suspicions immediately landed on the network when he heard about the misdeed.
In Star Trek: The Battle of Betazed, the Vorta overseer Luaran objects to her colleague Gul Lemec casually shooting Betazoids during their occupation of the Betazoid homeworld. Like most Vorta, she has no moral qualms at all, but does not approve of needless violence when there are more orderly ways to keep things in check. As far as she's concerned, Lemec's brutality will only serve to increase resistance among the occupied Betazoids.
While Moriarty and Moran in Kim Newman's The Hound Of The D'Urbervilles are not above doing things For the Evulz, they often adhere to this trope. At one point, Moriarty researched stealing the Crown Jewels of Britain, but rather than actually pulling the caper, sells the plans to the guardians, so they may tighten their security. And Moran discourses at some length about the foolishness of criminals who steal unique, one-of-a-kind, well-known (or religiously-venerated) valuables, because they're impossible to fence and often bring retribution after the thief.
In Alien Nation, Aphossno, the overseer scout, helps Cathy do develop a therapy against a genocide-attempt by genetically engineered from a "Purist" (Anti-Tenctonese hate groups) group. He does that, because the overseers can't profit from dead "cargo" (He plans not only to re-enslave the former Tenctonese slaves, but also to enslave humanity, since the overseers military technology, according to the overseers, is vastly superior).
In the words of Jimmy Darmody: "You can't kill everyone, Manny. It's not good business." Of course, Jimmy's temper and ruthlessness sometimes means that he takes steps that make everyone else think he is going too far and being impractical himself...
Both Arnold Rothstein and his Bastard Understudy Meyer Lansky are tremendous examples of this.
A humorous version of this comes up in season 6, when a vampire refuses to drink Buffy's blood because she's been eating a lot at a crappy fast food joint. Eating her at that point would likely make him feel sick.
An earlier episode had someone spared because the taste of steroids in his blood disgusted the vampire. Also, they were special steroids that were slowly turning him into a fish, so it's understandable.
Mayor Willikins was equal parts Affably Evil and this trope.
Scorpius from Farscape is incredibly goal-oriented, and rarely lets petty things like "emotions" get in the way of his mission. Thus, even when John Crichton has utterly demolished his base, ruining his plans for revenge against the Scarrens, he states the following when John asks if he is considering following through on his earlier threat to glass Earth.
Scorpius: To what purpose? Vengeance against you? The only vengeance I cared about is no longer within my grasp!
Cersei is clearly appalled by Joffrey's decision to have Eddard executed, knowing that leaving him alive is the only way to prevent war with the North.
Later on, her father, Tywin Lannister, saves a group of prisoners including Arya Stark, although he doesn't seem to have realized it, from torture and death. Not because the whole torture thing bothers him, but because, hey, why waste free laborers?
In Kaizoku Sentai Gokaiger, Basco ta Jolokia is perfectly fine with letting kids die, blowing up schools, and even killing his own Morality Pet to get what he wants. However, he decides to spare (and in one case, save) the Gokaigers because they're all after the same treasure and it's easier to let them do the heavy lifting for him* Especially since the last "key" to the treasure is held by a group of ninja who don't want Basco to find them but do want to help the Gokaiger.
The Ferengi are a Planet of Hats based on greed. They'd never practice mass slavery or genocide-because people who are enslaved and/or dead can't buy things, although they don't mind selling to those who do practice it. One of their first appearances even uses this to invoke the "what profit vengeance" Aesop, with one revenge-consumed DaiMon's crew deposing him for wasting their resources, and thus depriving them of profit, in an attempt to get revenge on Picard.
The Female Changeling gets an instance of this near the end of the series. The Dominion have just gained the Breen as allies, who have a weapon that totally disables any ship it hits. This decisive advantage allows the Breen to defeat a combined Federation/Klingon/Romulan armada, including the Defiant. Once everyone's stuck in escape pods, the Changeling orders them spared. Not because she cared, but because their effect on morale to their enemies was worth far more than their deaths. Then again, given Sisko was among those in the pods, she might not that thought that through entirely.
One Starfleet officer note the Cardassians would not go to war with the Federation, or even ramp up border security, after one of their ships blew up. They are very happy with the peace treaty they have with the Federation, it gave them a land expansion, and now have colonies on the federation side that they know will be taken care of and used as spies, so would not risk losing it for such a small incident.
Star Trek: Voyager uses this trope as a Take That against the Kazon villain race from the first season. When an off-hand comment about them is made in front of Seven, she recalls how the Borg ran into one of their colonies. They refused to assimilate the colony because it would detract from their perfection. They didn't even have desirable physical qualities. Even the Talaxians got praise for that.
Played straight in Season 2 when The Greek and Vondas contemplate killing Frank Sobotka, not out of genuine malice but rather because police are using damning evidence of his corruption in order to turn him for the prosecutionagainst them. Vondas convinces The Greek it would be more pragmatic just to buy Frank's loyalty (and silence) by manipulating Frank's son Ziggy's murder trial and preventing a conviction. Unfortunately, Frank had already made a deal with the FBI by then, and both The Greek and Vondas find out from a "friend" in the FBI while Frank is on his way to meet with them. Frank is shown with his throat sliced open in the beginning of the next episode.
The Greek: "Your way... It won't work."
Similarly, in Season 3, once Stringer Bell took over Avon Barksdale's drug empire, he negotiated with other Baltimore players to create a co-op; his period of control marking what was almost certainly a low point in violent drug-crime, since it wasn't in the best interests of any of the dealers. Stringer had also been taking economics courses, and so this pragmatic course of action was a solid application of coordinated action to avoid the "tragedy of the commons". Unfortunately for them, Marlo's refusal to join their cartel and continued use of violence also solidly illustrated the free-rider problem and "prisoner's dilemma".
A more minor example is Dennis "Cutty" Wise. Cutty was a street soldier who has finally been released after a long stint in jail and gone to work for the Barksdale gang. When Cutty and a couple of other Barksdale enforcers catch a dealer stealing money from the organization, a No-Holds-Barred Beatdown begins. In the middle of it, Cutty begins to protest, saying that if they beat him too badly to work, how is the dealer ever going to pay them back what he owes? The young thugs keep going anyway, beat the dealer to death, and steal whatever money and bling he has on him.
The various gangs in Sons Of Anarchy sometimes set aside blood feuds in favour of profit.
Supernatural: Every time a Deal with the Devil is made, the victim is supposed to get to live for 10 more years before the demons come for him. Crowely is outraged when a lesser demon comes for his victims early:
In Dick Tracy, the final Big Boy Caprice story by Max Allan Collins has him trying to kill Tracy with a million dollar open contract on the detective. Eventually, the organized crime ruling committee, The Apparatus, confront Caprice and tell him that the contract must be canceled. In this case, this is not motivated by moral considerations, but as a matter of professionalism considering the fact that Tracy has learned about the mob contract on him and has taken personal control of the department's Organized Crime Unit to retaliate. The Apparatus knows that they can't afford to let Tracy come at them full bore and so they must take action.
Velor Vedevix of Cerberus Daily News was a pirate and slaver before the Reaper invasion. Once the true magnitude of the threat was revealed, he began focusing his efforts on fighting the Reapers, gathering other pirates to fight, scavenging in the Terminus systems, even openly delivering needed supplies to Alliance warships that would have happily blown him out of space a month earlier. If the Reapers win, no more piracy.
Illithids in Dungeons & Dragons have to be pragmatic since their powerbase is a mere shadow of what it was in their glory days. Illithids would like nothing better than to gorge themselves on humanoid brains, but most of them are smart enough to realize that indulging their appetites too frequently would bring the wrath of every other humanoid race upon their tentacled heads. So the Illithids limit themselves to one or two brains a month while engaging in backroom deals, slave trading, and subtly aiming for power in the shadows.
Blue and or black villains in Magic: The Gathering tend to abide by this. For example, in the Odyssey and Onslaught cycles, the Cabal is a ruthlessly evil organization that is, nevertheless, primarily interested in profit, and the Cabal Patriarch recognizes that certain types of evil are...wasteful.
The Tau are (besides the Card-Carrying Villain that is Chaos) the only faction that do not have "All the aliens must die, sooner or later" as policy, and are willing to incorporate other species into the Empire - sometimes at gunpoint, but other times a species will willingly join the Tau.
Although, considering the alternatives are either being eradicated or turn to the fun times of Chaos, joining the Tau is the only smart thing you can do in the galaxy.
The Dark Eldar was made into this to explain how a bunch of Neutral Evil backstabbers were still alive after 20,000 years.
Indeed, every faction in 40k are pragmatic villains; Dan Abnett pointed out that if Chaos really was a "nail a baby to your helmet" society as some claim they would simply collapse in on themselves and be destroyed within a week. As such, even the most villainous 40k factions must, by definition, have a functioning society. Since they can all threaten the Imperium to a greater or lesser degree, that means there must be people who can engage in pragmatic villainy. Any examples (from any race) that contradicts this can therefore be dismissed on the grounds of "every sufficiently large organisation has a bloody twit in a position of power."
In Rifts, the Vampire Kingdom of Mexico. Their Master Vampire is evil and ruthless, but he's Lawful Evil and understands the value of keeping a contented blood supply around, and thus the Kingdom is actually one of the safest and most peaceful realms on Rifts Earth. Blood is provided through a painless system of blood donations, staggered to avoid causing harm to the humans who donate, and vampires are forbidden from attacking humans to feed (though they still tend to be dicks toward them; they are, after all, nearly always evil). In part because of this system, Mexico is the most powerful and advanced of the Vampire Kingdoms.
In Werewolf The Apocalypse, even other minions of the Wyrm will destroy any Gray Mass infestation that shows up. Their corruption is so virulent and indiscriminate that they even jeopardize the other minions of the Wyrm and the Wyrm's greater plans.
Super Mario Bros.' Bowser. At times he helps the Mario Brothers and other people, only because he wants to be the only one to take over the Mushroom Kingdom. Also, since his goal is conquest and not destruction, he'll assist the Mario Brothers so that others can't destroy what he wants to conquer.
Caster in Fate/stay night refrains from actually outright killing the victims she drains because that would draw even more attention, too much to cover up with a story about gas leaks.
The Agency of Hitman normally go after criminals and the like due to the fact that people pay more for world stability. Also, Agent 47 prefers not to kill anyone not his target, since collateral damage isn't professional and it creates the risk of more witnesses.
This is the reason why "professional" pirates in Eve Online hate the more Griefer-like rat bastard ones. A professional pirate will trap your ship and make you a simple offer - pay them or your ship and capsule will be destroyed. If you pay up, they'll let you go, otherwise they blow you up and loot your wreck. The rat bastards will do the same thing, except if you pay up they destroy you and loot your wreck anyway. The professionals hate the bastards because they make people far less likely to pay up, which is far more reliable profit than looting wrecks (as what survives a wreck is random). Quite a lot of people in Eve refuse to ever pay ransoms for their ships simply because they don't believe in "honest" pirates any more.
"The Practical Incarnation" is the name for the most evil of your previous selves you encounter in Planescape: Torment. Everything he did had a practical use, even if it ultimately resulted in horrible things like convincing a woman he loved her so her very soul would stick around and act as an oracle for him. He even leaves you with some very good, easy-to-follow instructions, so much the better to make sure you can carry on his work even after his death.
Mr. House is not a nice man and freely says that he desires to become the region's dictator (he prefers "autocrat"), but he has no interest in power without a purpose and his plans for the Mojave would certainly benefit mankind as a whole. Likewise, he's merciless in dealing with people who have earned his ire or even have a chance of standing in his way, but in personal interactions he's usually just sort of condescending, not showing any overt malice.
Father Elijah, a fanatic, actually had some pretty sensible policies during his time as the leader of the Brotherhood of Steel, including obtaining beneficial technology such as farming equipment and trading such technology with wastelanders in order to gain their support. Elijah doesn't care about wastelanders and is happy to sacrifice them if needed, but was smart enough to recognize that the Brotherhood was too small and insular to survive without support from their wastelander neighbors (a fact which even his much more moral successor completely missed). Or not. His successor can be made to admit that the Brotherhood is doomed, but he's not willing to break the Codex like Elijah was. Elijah breaks the rules for what he sees as the greater purpose of his organisation... both the ones that keep the Brotherhood from being outright evil, and the ones that have long lost their purpose in the modern wasteland.
The Khans are a group of raiders that act like "professional" pirates. They're mainly hostile to the NCR, but tend to ignore locals of the Mojave, and are willing to trade, though the only thing they have to trade is drugs (though they will sell weapons to the Courier if s/he manages to get on their good side) and by the time of the game mostly keep to themselves at Red Rock Canyon.
In the final battle, Legate Lanius will only consider retreat if he's properly convinced/bluffed that it is the better decision either due to the fact that the Legion lacks the ability to properly sustain itself that far, that he is secretly being set up for a trap much like his predecessor Joshua Graham or some other reason that would make sense to him.
Colonel Moore is this. She is willing to put up with anything the Courier does because it will lead to winning the war, but she makes sure to slander the Courier and gets Ambassador Crocker fired for doing things their way instead of hers.
"Good" choices in Overlord are often framed as this. For instance, after retrieving a village's stolen food supply, you're given the option to take it to feed your horde—but giving it back to the villagers instead increases their productivity (represented in-game by a higher respawn rate for the sheep you kill to feed your basic troops.)
In the Deus Ex Human Revolution "The Missing Link" DLC, you can find an email from the evil base commander where he claims he was informed that his subordinates are raping their female prisoners and demands that they stop or face harsh punishment...because this decreases the chance that they survive the horrific surgical procedure that turns them into Hyron Drones.
Flemeth of Dragon Age is a mysterious shapeshifting "witch of the wilds" and an Evil Matriarch besides, but she scoffs at the stories of her kidnapping and eating children. "Pah! As if I had nothing better to do!"
Considering the events near the end of the previous game, Agatio also seems to be much more tolerant of Felix not directly following their plans than his predecessors were. Though he's pretty rough about reminding Felix what's at stake, he doesn't turn on Felix until Felix acts against him on behalf of Isaac, and even then he bides his time until Felix has finished his part and is no longer needed for the plan to succeed.
PAYDAY: The Heist has this for the heist crew. They don't want to kill civilians because it will make the cops more aggressive against them. In a gameplay perspective, you don't want to kill civilians because doing so delays your release from police custody, gives the team less hostages to work with, and you incur a monetary penalty at the end of the level.
In the prequel series Start of Darkness, Xykon says he will not do any scheme of kidnapping virgins because "it's like giving a guy who doesn't know how to hold a hammer and making him to build a house for you". He also thinks that destroying the world is a stupid idea, because if he did that, what would he have left to rule? "I like the world... I'm certainly not about to destroy it unless I get really, really bored."
During a story arc in the main series, an imp suggests that Vaarsuvius use some virgin's blood as a spell component, which is rejected for three reasons:
Vaarsuvius : This is reprehensible, depraved, and most importantly, highly impractical given our current location.
Tarquin, who claims to be Above Good and Evil, runs the Empire of Blood. His interaction with Heroes suggests he's so Dangerously Genre Savvy it hurts, including knowing world domination is rather hard to pull off if everyone knows you're doing it. He even offers help and magical rewards to prevent Xykon from doing so either.
Belkar, amazingly enough, manages an instance of this, after one of his shoulder demons convinces him that saving Hinjo's life will work out better for him in the long run than letting him be killed by an assassin.
Dark General Cobalt of Sailor Nothing is this in contrast to his Card-Carrying Villain acquaintances. It's not that he has a moral objection to rape, torture, and murder, it's just that he finds it a colossal waste of time. He'd much rather focus on getting things done. Interestingly, his pragmatism actually results in his being the villain the heroes encounter the most—in the interests of actually getting his project off the ground, he decides to kill the girls who've been wiping out his underlings.
Troops following Lord Doom, an Evil Overlord from the Global Guardians PBEM Universe, are under strict orders to protect innocent bystanders as much as possible and keep collateral damage to a minimum during their operations specifically because the villain believes that such activities are a waste of time and "bad for business", since loyal, happy subjects who feel their Lord and Master is looking out for their safety engage in rebellions far less often than fearful, unhappy subjects who feel their Lord and Master tortures them for his own amusement do.
Quite a few characters in the Whateley Universe have shades of this. Take Mimeo — with his shapeshifting and power-copying abilities and definite intelligence, he could readily become a dangerous Hero Killer if he ever put his mind to it. (He is on the record as the sort of villain that can confidently take on entire teams and expect to win.) Instead he's quite content to fight a bunch of opponents for a while to acquire their powers, then use those while they last to pull off his real scheme, and then do a vanishing act to enjoy his ill-gotten gains; that approach has been working well for him for years by now and as far as he's concerned he has no reason to change it.
One episode of The Spectacular Spider Man has the eponymous hero confront Tombstone after beating up a pair of his Mooks. Tombstone lands a few good blows on Spider Man and seems poised to give him the beating of his wall-crawling life, but instead calls the police and informs them that Spider Man just trespassed, assaulted his employees, and threatened his well-being. These all being valid facts, the police try to arrest Spider Man while Tombstone sits back and watches.
Shere Kahn in Tale Spin once made certain that his workers were freed from a corrupt underling who was working them to death.
Shere Khan: My dear, I desire only money and power. Unpresentable employees provide me with neither.
Batman The Animated Series: This was the reason Ra's al Ghul deposed his son Arkady Duvall as a potential heir to his world-conquering empire; Ra's' entire shtick is his belief that Utopia Justifies the Means, which includes making sure The Trains Run On Time, so the prospect of using barbarous and inefficient tactics to ensure that (such as whipping hard workers for every little slip-up, or disposing of supposed interlopers by dunking them in molten lead, as Duvall does in the episode "Showdown") does not sit well with him, at all.
Blob and his men themselves often are very pragmatic, while it's perhaps more out of cowardice than strategy, they rarely ever directly attack the heroes and most of their plans involve the bare means to get the stone from them. In some episodes this actually makes them seem less antagonistic to the heroes than vice versa, who have a much more vengeful streak.
The same series also presented Dr. Doom in this manner during the adaption of the Secret War. While the other villains brutally conquer the planet the Beyonder has send them to and enslave the population, Dr. Doom turns the part of the planet that he manages to conquer into a peaceful paradise where robots do all the hard work and the population can live in luxury. His motivation for doing so is that the planet has technology far beyond that of earth (including a way for Doom to heal his disfigured face and cure Ben of the Fantastic Four of being stuck in his monstrous form), and by destroying the civilization or ruling as a tyrant, Doom would only deny himself access to this technology.
Xanatos from Gargoyles never carries the Villain Ball; his plans are pretty much designed so he HAS to win something. He also refuses to engage in revenge, because as he sees it, it's a "sucker's game" with no real benefit, and seems to want to remain friendly with his enemies, since he could easily need their help someday. A good example of this trope is in "Enter Macbeth," when he's reluctant to kill the gargoyles during their stone sleep not because they're defenseless, but just because it "seems like a waste." The same episode has Macbeth calmly wait for them to wake up before trying to capture them, since that, after all, is the honorable thing to do.
Agent Bishop in the 2003 Teenage Mutant Ninja Turtles. He had the goal of protecting humanity from aliens, and while he was extremely ruthless, he had his priorities in line and didn't go and spend time trying to kill the turtles, who were ultimately more an aid to him then a hindrance.
Although he hates Darkwing Duck and would be happy to get rid of the interfering superhero once and for all, Megavolt has helped DW on one or two occasions when the city of St. Canard is at risk of being destroyed. He justifies this by pointing out that if St. Canard is destroyed, there will be nothing left for him to rob.
One of the lessons Megamind learns after apparently killing Metro Man. Part of the enjoyment of being a supervillain is having a worthy superhero to do battle with.
Dracula from The Batman Vs Dracula doesn't like to kill his victims, but not because he doesn't like killing. He just hates wasting a life that could be better used as his undead servant.
Beast Wars: The Tri-Predacus Council, leaders of the majority of all Predacons, sends an agent to prehistoric Earth to aid the Maxials and capture Megatron, whom they declared a dangerous criminal. They, like Megatron himself, still want to take over Cybertron and spark a second interstellar war, but would prefer to do so through subtle manipulations and waiting for the opportune moment. That and Megatron's plan is too reckless even for them to consider.
Soundwave of Transformers Prime has made a career out of this. It diminishes his effectiveness not the slightest.
Imperiex of Legion Of Superheroes winds teaming up with his Arch-Enemy Superman X in order to protect a young boy from some contract killers, if only because that young boy will be the one to invent the technology that would create Imperiex in the future.
In Ben 10 Alien Force, Vilgax's return episode portrayed him as following a galactic code of conduct. However, Word Of God is that Vilgax was only following it because it was more profitable for him, allowing him to conquer ten planets in a short amount of times without wasting massive resources to it. In later episodes, after this strategy failed against Ben, he has no scruples breaking said code several times.
Dr. Heinz Doofenshmirtz in Phineas And Ferb wants to take over the Tri-State Area, but he prefers to use complicated and overly-specialized "inators" rather than break out a weapon which could do real damage. His rationale is that, if he destroys the Tri-State Area, there won't be anything left to rule.
In the first episode of Family Guy Stewie mind controls a judge to acquit Peter of fraud and give him his job back because Stewie relies on him for food and a home.
While Sir Hiss from Robin Hood seemed genuinely shocked that Prince Johnwould execute Friar Tuck to lure Robin Hood out, he was probably afraid that doing so would risk of them being excommunicated by the Catholic Church, a powerful political entity at that time.