The averagely-skilled friends of the highly-skilled hero survive their encounter with the Big Bad or Dragon because the bad guy couldn't be bothered finishing them off. Whether or not this makes any sense as an excuse to keep the secondary protagonists alive varies. Sometimes it's an excuse from a Worthy Opponent or Noble Demon to not engage in wanton slaughter. Sometimes the villain needs to remain stealthy and realizes that a large body-count does not aid that. Sometimes the heroes fit into an Evil Plan of the villain that requires their survival (for the moment). Sometimes the villain figures that the would-be victim is actually a net liability to the heroes or a potential convert to the villain's cause.
The most literal examples of the trope refuse to kill their targets for the same reason a normal person doesn't hunt down and stomp on every cockroach they see; it's just not worth the time and effort unless they're making a nuisance of themselves. This usually applies to villains arrogant enough to believe that the heroes aren't a real threat, or powerful enough to know that they aren't a threat. Genre Savvy heroes should be aware that a villain can and will change their stance if they cause enough trouble for them.
Also sometimes used by the Anti-Hero as an excuse for not wiping out the Mooks. May be related to Doesn't Like Guns. Compare Cruel Mercy, You Will Be Spared and Villain's Dying Grace.
Goku subjects Fieza to this during their fight on Namek. He fights until Frieza is no longer a challenge, then throws that fact in his face, believing that living with the shame of being defeated by a superior fighter was a far worse punishment than simply killing him, made worse by the fact that said superior fighter was "just a monkey." Frieza, however, isn't about to give up so easily.
Mr. Satan "fights" Perfect Cell and is simply backhanded a few hundred feet backwards into a mountain. He inexplicably survives (Piccolo suggests Cell didn't want to waste a single drop of energy when he was about to fight Goku).
In Bleach, Ulquiorra took this line with Ichigo after their first confrontation, but later acknowledged him as someone that "needs to be eliminated" and started fighting him more seriously. Ichigo turns this around with his Super-Powered Evil Side and performs a No-Holds-Barred Beatdown on Ulquiorra.
In fact, about half of battles in Bleach end with the winner leaving the loser alive because they're 'not worth killing'.
In Gundam AgeDecil gets bored seeing a UE mook clearly beating the Gundam Titus in episode 8 and orders the UE to retreat.
In Tokyo Babylon and X1999, Subaru, the protagonist of the former, is left alive by the Sakurazukamori because Seishirou explicitly tells him that he's not worth killing. This becomes Subaru's primary motivation in the sequel; he believes he can only be worth something to Seishirou (who he loves) if Seishirou kills him. However, as it turns out, it's not that Subaru isn't worth killing - it's that Seishirou wants Subaru to kill him.
Part of Sasuke's backstory in Naruto is that this was why his brother spared his life alone among the extended family. Or so he believed for years.
Sasuke also gives this excuse for not killing the mooks he faces in his quest to kill his brother.
Mirielle says this to Altena in the last episode of Noir, specifically that it's "not worth soiling a bullet" with her blood. Altena then tries to shoot Mirielle, but Kirika jumps in and tries to pull a Taking You with Me, though Mirielle manages to grab her in time.
Phoenix Ikki from Saint Seiya delivers this line to Sea Dragon Kanon at the end of the Poseidon Saga, throwing the pointlessness of his plan in his face before turning his back on him and walking away. Kanon tries to retaliate, but fellow Marine Shogun, Siren Sorrento, confronts him after hearing the truth behind Poseidon's premature resurrection. Like Ikki, Sorrento reasons that Kanon is so pathetic and worthless that fighting him would be a dishonor to Poseidon.
Hal in Texhnolyze tells this to Shinji after being turned into a Shape, musing on his earlier promise to kill him when they next time met.
In Code Geass, this is probably the only reason Tamaki survives any given battle.
And in the penultimate episode, Diethard is not worth Geassing.
Fushigi Yuugi has Miaka's ex-best friend Yui justify (in both of Miaka's visits to Kutou, mind you) that she only wants to keep Miaka and the Suzaku Seven alive because after all, "Where's the fun in killing them right away?" Yeah right.
Death Note's Light doesn't really target the regular Joes in the task force, figuring that they can be hoodwinked easily enough and besides, they're decent enough people. (The fact that his father is a part of said task force probably has something to do with it, too.) When Aizawa catches on, though, they pretty much all have to die when Near does.
Invoked in Fist of the Blue Sky, when a mook asks a mob boss and a French general about his share of the money of a drug operation and finds himself held at gunpoint by both of them. They discuss the thing and agree he's not worth the price of a single bullet... And then they shoot him anyway.
Adolf Hitler is spared by Liu Zong Wu because he thinks the tyrant is far too pathetic to deserve a good beating.
Younger Toguro spared Suzuka, Bui, and Karasu in YuYu Hakusho. He said Suzuka was a pathetic and spineless coward, who was not worth killing. He made the other two serve him and join his Dark Tournament team. Averted with his brother. Elder Toguro says he will spare one of the two defeated team members that lay before him in the semi-finals. One begged for his life and was instantly killed. The other says he would rather die than do the same. Toguro says that his brother would let him live, but he won't and finishes him off.
Magical Girl Lyrical Nanoha Strikers, The Huge attack on the TSAB's Headquarters left destruction of property, wounded many troops and main characters alike, and kidnapped two secondary characters. They let no one died. This bites them hard in the end when the wounded main characters was the turning point of the final battle and this is when they decided to drop the trope.
InuYasha: When Inuyasha was controlled by his Superpowered Evil Side and killing bandits right, left and centre, it took Sesshomaru to bring him down. To the gang's surprise, instead of killing Inuyasha, Sesshomaru merely tells them how to reverse Inuyasha's condition. When Miroku demands to know why Sesshomaru spent the entire fight holding back against Inuyasha and refusing to kill him, Sesshomaru simply responds that there's no point in killing someone who's in no condition to know even his own self. He also adds that he'll kill Inuyasha when he's ready. He never does.
Weed from Ginga Densetsu Weed would often spare a bad dog's life, saying that they're not worth killing and murder is wrong. A few dogs in his own pack call him out on this...especially Kyoushiro.
Hiro decides this with a recently beaten Kamikiri, who's been castrated brutally, and says that he's only showing him mercy one time. Kamikiri tries to attack the Great Pyrenees once more, but...surprise, surprise! His fangs were ripped out! And it's been confirmed that he died from his wounds.
In A Certain Magical Index, the amoral psychopath Teitoku Kakine occasionally does this, because he feels it would be beneath him to waste energy on someone who is completely helpless or already dying. An example is when he is attacked by Rikou Takitsibo, whose powers are fueled by taking the drug Body Crystal, which slowly kills its users.
The Ice Maidens in YuYu Hakusho were shocked and aghast that one of them gave birth to a boy (which meant she had contacted a male: strictly against their strict isolationist policy). Said boy (Hiei) was cast down into Demon World proper and left to fend for himself. After some ordeals in the past, he located the sky island where they lived, seeking revenge. Ultimately, though, after seeing their cold, emotionless lives with his own eyes, he declares them to be not worth his time and leaves them to their pathetic existence.
In the Astro City story "Great Expectations," actor Mitch Goodman (who plays the "Crimson Cougar" on a soap opera) is ambushed in public by the Dark Centurion, who easily pummels him. When Mitch begs for mercy, the Centurion sneers that he's Not Worth Killing and leaves. It was a ruse set up by Mitch and his friends so Mitch could stop being a high-profile celebrity super-villain target.
In the MarvelTransformers Generation 1 story "Target: 2006", Galvatron decides not to kill Ironhide on the grounds that such a pathetic specimen simply doesn't deserve to be killed by one as great as him.
In Fables, Baba Yaga and the djinn find themselves trapped in the business office with Buffkin, Frank, the mirror, and some of the barleycorn brides. Buffkin challenges Baba Yaga and the djinn, but they just laugh at him and float away. This has some consequences later. Snicker snack, indeed.
The duology begins with a nifty subversion. Upon discovering that in spite of their vicious assassination attempt, the Bride is still alive though in a coma, Bill refuses to let Elle kill her because he thinks so highly of her and doesn't want her being killed like "some rat" in her sleep. He says that if she ever wakes up, they'll finish the job. She woke up alright, and she was pissed.
Inverted, where The Bride hacks her cold-blooded way through literally dozens of sword-wielding Yakuza foot-soldiers, then decides one of them, a young teenager, is too pathetic to kill. She puts him over her knee, spanks him with the flat of her sword and tells him to go home to his mother. He flees.
Seen in the Peter Cushing/Christopher Lee movie Horror Express. The brainsucking alien finds the crazy monk not worth killing, and eventually the crazy monk starts worshiping the alien (which the alien finds somewhat annoying).
Crazy Monk: "Are you going to kill me?
Brainsucking Alien: "Oh, there's nothing in your head of any use."
When the Spanish ships sail by Barbossa's in Pirates of the Caribbean: On Stranger Tides, they don't so much as spare him a glance, even though their numbers would have easily allowed them to sink his ship.
In Alien vs. Predator, at one point one of the Predators has a chance to kill Charles Bishop Weyland, but instead turns away, due to Charles' terminal illness meaning that he's not a threat and thus not worth killing. Charles gets offended at being ignored and fires a makeshift flamethrower at the Predator. The Predator then kills him, either having re-evaluated him as a legitimate threat or simply being pissed off at having been set on fire.
In Predator Dutch is about to smash the mortally wounded Predator's head with a boulder but then changes his mind and apparently decides to leave the creature to die on its own. The Predator then demonstrates why following this trope can be a really bad idea, when he activates his self-destruct mechanism, and Dutch barely escapes the resulting explosion.
In Breaking Dawn Part 1, when Bella is feared dead, Jacob blames Edward and tells him to his face, "I won't kill you. That would be too easy. You deserve to live with this."
In Batman & Robin Poison Ivy is about to kiss Commissioner Gordon before deciding to spare him, saying that he's way too old for her.
In The Crossing, General Howe doesn't want to bother with finishing off the Continental Army in the middle of winter, so he leaves a small force of Hessians to keep an eye on them while he and his army winter in New York. Washington is incredulous, and also, insulted.
In Tamora Pierce's Daughter of the Lioness, Vereyu kills the recently-appointed spymaster (who's not really sympathetic, just incompetent, but you do kind of pity him). The heroine, AlianeCooper, tells her that he was "not worth killing". Vereyu retorts that he "wasn't worth leaving alive, either." Aly remarks that that's true.
This basically saves Rincewind's life and the world in Sourcery when tries to attack the nigh-omnipotent sourcerer Coin with a half-brick in a sock. Coin is so fascinated by the idea of someone trying to use a weapon that feeble against him that he defies his father's orders to kill him.
Mahou Sentai Magiranger (Power Rangers Mystic Force) has a subversion: Wolzard (Koragg) has a suppressed good side which leads to him finding excuses to let the Rangers live, the main one being that it's dishonorable to slay an unworthy opponent. When a Ranger confronts him, Wolzard gives the standard 'unworthy opponent' speech, and the hero responds with a volley of lighting bolts. Wolzard is completely unharmed, but decides anyway that the hero's worth fighting after all, and proceeds to utterly mop the floor with him. (He still lets him go in the end.)
As it turns out, Cromartie does this because he believes Ellison will lead him to the Connors. However, in a recent episode another Terminator leaves at least one minor character alive because, as the audience sees through the Terminator's vision, the character has a threat level of "none". In what may or may not be a subversion, the same minor character is (apparently) killed later in the episode by the same Terminator - offscreen. Granted, this was (apparently, this part was also offscreen) after he unloaded a Mossberg into said Terminator, which presumably upped his threat level a tad.
Also, in most of the Terminator films, Terminators have a habit of hijacking a vehicle, then ordering the driver to "get out". Presumably, scaring the driver out of the vehicle is less time consuming then killing him and dumping his body outside.
Or, the person could simply be deemed a "waste of ammo" as a Terminator decided that Guns N' Roses were in a music video the group released for the second movie.
Or that in the time it would take to kill the driver/pilot, it might lose track of its primary target.
Cameron later explicitly tells John (after being confronted with an empathy test) that Terminators are not designed to be cruel. Which makes sense, being unfeeling machines they think logically and practically, simply following their motivations. Interpreting an action of sheer pragmatism as cruel or benevolent is something only a human would do.
Played with in Burn Notice. Michael Westen takes great pains not to kill anybody himself—often employing elaborate Plans instead—because a body count would draw too much heat while he tries to clear his name. A few people are worth it, but the consequences are still generally unpleasant.
Horatio Hornblower: Horatio tells his opponent in a duel Jack Simpson that he's "not worth the powder" after Simpson has fired prematurely, claiming it was a misfire, wounding Horatio and giving him a free shot. Simpson then begs for his life like a Dirty Coward. The minute Horatio turns his back, however, Simpson attempts to stab him In the Back. Captain Pellew can afford the powder and shoots Simpson with an exceptionally fine shot.
In the Supernatural episode "Time Is on My Side" Dean tracks down Bela with the intent to kill her, before announcing that she's "not worth it."
Game of Thrones. At the beginning of Season One and the end of Season Two, the White Walkers leave a single member of the Night's Watch alive, either to spread fear or as an example of this trope.
The Vampire Diaries: For much of the third season, the good guys depend heavily on Klaus not bothering to kill them, which he could do pretty much any time he wanted.
Non-fatal variant in The Thick of It - when Ollie informs his Mean Boss Malcolm that a disgraced former MP is here to see him, Malcolm rounds on Ollie, delivering him a metaphor about how when the Queen's butler sees a cockroach in the kitchen, he steps on it and she never knows. When Malcolm does eventually go and speak to the MP, he treats him with weary contempt rather than his characteristic foul-mouthed ranting, suggesting he finds him beneath even a bollocking.
Buffy the Vampire Slayer: In season 4's "Doomed," Xander, during his Breaking Speech to Spike, remarks that he knows that he could easily kick Spike's ass as a result of his being chipped, but he's so pathetic right now that he's not even worth the effort.
In TravellerIntersteller Wars the Vilani don't bother making a real effort to subjugate the Terrans because they are "just another barbarian tribe". By the time they learn differently it is the Vilani who are being subjugated.
Subverted in Silver. Having destroyed the source of the titular' villain's power the hero feels like sparing his life cause he's all old and pathetic now, but the Silver's Nemesis arrives and finishes him anyway. Somehow the hero has no qualms with that. Huh.
In Sonic and the Black Knight, after Sonic's first showdown with King Arthur, the king remarks that Sonic is "a fool of a knight not even worth slaying" before departing. This bites him in the ass later on, as Sonic takes the opportunity to learn and grow stronger in order to defeat him.
In Grand Theft Auto IV, the main character Niko Bellic comes face to face with the man who betrayed his group in the Balkans and killed his village for money in Balkans war. The man is flown in and is in a pathetic state, barely even sane and you can choose to either execute him for crime, or spare him. If the latter is chosen, Niko concludes that he is indeed not worth killing and deserves to be left alive to suffer, while in the former case, Niko brutally kills him, only to find that Vengeance Feels Empty.
Metal Gear Solid: Portable Ops has a scene where Python encounters General Skowronski in the bottom of a warehouse while hunting for Big Boss. After defeating Skowronski, Python freezes him inside a cage and exclaims "You're not worth killing!" before leaving. Snake frees the general minutes later.
The eponymous villain of the Wrath of the Lich KingWorld of Warcraft expansion. After being hyped up in the months before the release as being a villain whose threat will be felt throughout your travels instead of just "a meaningless name until you suddenly face him at the end" (the expansion is called The Wrath of the Lich King, for pity's sake), every time you meet him he lets you live, either knocking you out or just giving you a stern warning, while first killing his minions left and right for their failures to kill you. He always says something like "You are barely beneath my notice" or "Perhaps in time you will become worthy of serving me." He does have ulterior motives for keeping you alive. When players finally confront and almost defeat the Lich King, he uses Frostmourne to wipe out the players, and reveals his true plan; everything up to that point was a test to find the strongest warriors in Azeroth, and lure them to Icecrown where he kills them and raises them as Elite Mooks in his undead army.
He had done it earlier in Warcraft III: The Frozen Throne as well: After severely wounding Illidan near the Frozen Throne, Arthas didn't finish him off. The game's sound files reveal that he considered Illidan a piteous creature who wasn't worth killing.
In Starcraft, one of the Zerg missions has you directing Sarah Kerrigan in an assault against Jim Raynor's headquarters on the planet Char. After razing Raynor's base to the ground Kerrigan decides not to kill him, proclaiming that he's not a threat to her....although it's possible and quite likely that she did it out of some remaining sentiment toward him. After defeating the UED base on Korhal, she decided that she had to kill both Raynor and Fenix. But after killing Fenix, she instead decided to spare Raynor again.
Warlord Okeer: "With that, I will inflict upon the genophage the greatest insult an enemy can suffer - to be ignored."
This trope also can appear in Garrus' loyalty mission. Garrus seeks to kill the traitor who betrayed his entire squad and caused all ten of their deaths. Once you track him down, you can help Garrus take the shot or talk to the traitor and warn him, where you learn he only did what he did because of a threat to his own life, and his life has been nothing but an empty shell of pain and guilt since. Garrus can be convinced to relent and stand down, and later says that he's okay with him living because Sidonis will have to live with that torment for the rest of his life, which he feels is a far better fate for him than a simple death. Later on, you can hear about how Sidonis eventually turns himself over to C-Sec out of guilt.
In his own loyalty mission, this is Jacob's opinion of his father — that he's not worth the price of the bullet it would take to kill him (and when you consider how ammunition in Mass Effect works, that's a very low price indeed). If prompted by a renegade Shepard, Jacob will change his position to "worth shooting, but I'm not going to do it".
In X-Men: Next Dimension, several characters use this as a taunt, including some such as Mystique saying another character isn't even worth her time. One of the first matches in the story mode could have her saying this to her son, which opens up a whole set of problems.
In The Elder Scrolls: Arena the Eternal Champion is left to rot in a dungeon, because his position in the Imperial Court was so low that the usurpers saw no need to bother. This was a mistake.
Rico: Considering the value of the Panuan buck, killing you would have been more expensive.
The AI in AI War Fleet Command starts out regarding the player this way, occasionally harassing them but otherwise leaving them alone. Much of the game is making sure the AI continues to believe this even as the player amasses enough power to turn the tide.
In the Sims 3, when a Sim with both the Unlucky and Loser traits gets into a fatal accident, the Grim Reaper will appear. Instead of taking the sim to the afterlife as usual, he'll resurrect your sim. His rationale is that it would be funnier for your Sim to continue on with his miserable, pathetic life rather than being granted eternal rest.
God of War III: When he runs into Hermes, Kratos initially holds this opinion of him, dismissing Hermes as "a fly from the ass of Zeus" that isn't worth his time. However, he reconsiders when Hermes decides to taunt him over how he killed his family.
Lampshaded in The Order of the Stick: During his second encounter with Roy, Xykon, the Dangerously Genre SavvyEvil Overlord, dismisses him as not worth fighting and suggests calling off the battle as a Mulligan, essentially offering Roy to go free so he can gain power and return later for a "good final tussle, Hollywood style". Roy rejects the offer, so Xykon kills him.
Mynd decides neither of the titular characters - demigod children imbued with fire explosion and electric powers, respectively - are worth killing, and even brushes George aside before trying to leave. This, inevitably, comes back to bite him in the ass.
Thaco:"You're not worth the XP I get from killing you."
Of course, by Dungeons & Dragons rules, Thaco gets XP for "overcoming the challenge" that Dellyn poses, so he's really not worth killing at that point.
In The Gamers Alliance, Ronove, the new Dreadlord of the Northern Horde, decides to spare the surviving defenders of the besieged city of Vanna and allow them to flee while the horde takes over the city. His superior and peers later question the merciful act as well as the fact that the survivors will inevitably spread news of the horde's activities and strategies to other cities which will be prepared for the upcoming war. He quickly justifies his actions by explaining his reasons for letting the heroes flee: their worthy opponent status, the promise of a later even bloodier battle worthy of higher demons' time, as well as the heroes' tales of the siege which will weaken other cities' morale when they find out about the horde's unstoppable might. However, the Dreadlord is playing a much more complicated game because among other things he also wanted to pay the defenders back for helping him when he was helpless by letting them flee to fight another day.
The Dimensional Guardians from the web fiction serial Dimension Heroes find themselves being spared from death multiple times, often by the Big Bad, who would much rather his servants take care of matters that are beneath him.
In The Salvation War there is a psychic woman who had been mentally tormented by a demon for her entire life. After the human army conquers Hell, she finds and confronts her tormentor... who turns out to be a teenager, literally a Troll From Hell, for whom driving a random innocent person insane was just a game (well, you know the kind). She's about to shoot him, but after seeing him groveling and wetting himself with fear, she decides that he is not worth pulling the trigger.
Ben 10: In one episode, after Kevin went around committing crimes and placing the blame on Ben, they end up in a showdown on a bridge. At one point, Kevin shifts back to his normal human form on accident and is completely at Ben's mercy, who is still using Fourarms. It seems like he's about to crush his skull with a well placed fist or two but instead hits right next to him before walking away, remarking that Kevin's not worth it and never was. This however, doesn't end up going well for him as he ends up needing to be saved by the guy who's been hunting him down the entire time due to Kevin's rage at being told this causing him to go One-Winged Angel.
On Robot Chicken the Yakuza kills all of **NSYNC except Joey Fatone, who was in the kitchen at the time. When he begs them not to shoot him, they tell him they wouldn't waste their bullets on a simple roadie.
Used in Futurama, except not with killing. Zoidberg teaches Cubert that the best way to avoid an ass-kicking is to pitifully grovel at the feet of a bully. It works surprisingly well.
The first time someone tried to release The New York Ripper in Britain, every single print got returned to Italy after the BBFC refused to classify the film.
On the Howard Stern show G. Gordon Liddy gave this as his reason for not holding a grudge or seeking revenge against his fellow Watergate conspirators (who had cooperated with prosecutors to get lenient sentences, leaving him hanging out to dry because he refused to do so).