Hathaway's Flash plays off of the Char's Counterattack novelization "Beltorchika's Children" rather than the anime movienote The main difference being that in the novel, Hathaway kills Quess; in the movie, Hathaway goes nuts and kills Chein after she kills Quess. And just to twist the knife further, after his death, Hathaway speaks to Quess's spirit, and she says she never loved him. So he fought and died for nothing. That's just cruel.
The death of Hinaichigo in the second season of Rozen Maiden. There was a whole episode dedicated to her winding down to her eventual 'death' where she spent the day with her old owner, complete with stuttered movement and speech during her last moments.
Her death in the manga, however, was still horrifying: Kirakishou used her rose vines to destroy and consume her from the inside out. Still sad.
Envy's death in Fullmetal Alchemist. He was a Jerkass who killed and tortured people For the Evulz, including beloved Ensemble Dark Horse Maes Hughes. What did it take to have people identify with him? A sad and horribly ironic death. He was brutally tortured by Roy Mustang and reduced to his pitiful true form before the good guys took pity on him. Edward even delivers an Alas, Poor Villain speech to his face, which disgusts him so much that he takes his own life.
And later? The murderer, Rolo, died too... and lots of fans mourned him instead of cheering because he sacrificed his life for Lelouch, even after Lelouch confessed his hatred toward Rolo, as the first and last thing he truly did of his own will. Lelouch himself ended up mourning him when all was said and done.
In Death Note, Kira Supporter Kiyomi Takada ends up getting kidnapped by Mello as a part of his Batman-Gambit to reveal Light as Kira. She's stripped naked by him and then kills him with a death note scrap she hid in her bra. Genuinely frightened and trapped inside a truck, she wraps herself in a bedsheet and then takes his phone and calls Light, asking him to come rescue her. Instead, he writes her name in the death note so that she commits suicide by setting herself on fire.
Misa's Scrappyhood, and her ending, which got past many people. In the close credits, she mirrors in dress and demeanor an earlier scene when she sings about her trust and devotion to Light. She follows the same route, ending at a veranda where she sadly and wistfully looks off into the sky, only this time she's standing outside the railing...
Kaname Tousen from Bleach betrays the Soul Society for a hypocritical reason (going the path with least bloodshed by joining the Big Bad). After being beaten by his vice captain and being reminded of his error by his best friend, Tousen seems to repent and wants to have one tender moment with his vice captain... then Aizen blows him up.
Not a death, but what befalls Momo Hinamori soon after this is this, at least in the western fanbase. She's not only impaled and nearly killed because of Aizen again, but this time, it's her childhood best friend and effective adoptive brother who's holding the sword, after Aizen uses his illusions to make him (and everyone else) see Momo as him.
Not a straight-up death example, but it happens in Pokémon. At the end of the Hoenn Story Arc, after Ash announces he's going to the Sinnoh League, May announces she's going to explore Kanto and compete in the various Pokémon Contests. Alone. Her little brother, Max, The ScrappyInsufferable Genius, is really put off by this, feeling like his sister is abandoning him. Sure, Max might have been irritating, but the way May told him to go home came off as a real dick move, and it's hard not to feel sorry for the kid.
For all his annoying tendencies, ineptness in reading his crew, responsibility in killing one of the more popular characters from the show, and overall nature, Nadesico's Admiral Munetake gets a pretty heart tugging send off. It doesn't hurt that much of the episode was spent humanizing him again.
To put more detail into this, Munetake was demoted due to the Nadesico's role in uncovering a Government Conspiracy (the enemies who were aliens are actually humans). Between the conspiracy itself, his demotion, and guilt over Gai's death, he falls over the Despair Event Horizon extremely quickly, expressing that he used to believe in notions such as truth and justice. His subsequent death/suicide (depending on how much you believe his rational mind still exists at that time) hits that much harder after all that.
In Shiki Masao Murasako got a lot of ire for being an annoying Jerk Ass, but then got an incredibly-sad death scene: he's so desperate for shelter from the vampire-hunters trying to kill him that he goes up to the house of his sister-in-law (whom he previously hated) and begsher in a small child's voice to let him in and not kill him. Instead, she takes advantage of the opportunity to beat him over the head with a pole and stake him through the heart. Even people who didn't like him thought the scene was very sad.
Made worse by the fact that he never could bring him self to actually drink blood from a person.
Let's not forget Chibiusa near the end of the Neherina Arc in Stars dies/becomes Ret Gone while Usagi holds her. It's also sad when realizing with Fridge Tearjerker that because Mamoru dies by Galaxia's hands, the last piece of Chibi-Usa we see is the remains of Usagi's memory/dream before everyone around her in the dream near the episode is gone.
Doug Ramsey, a.k.a. Cypher, from the X-Men family comic New Mutants was considered to be The Scrappy (due to his fact that his mutant power was the ability to speak every language, which sort of paled next to eye-beams and weather-control and the like), and fans repeatedly demanded he be killed off. Once he died, everyone missed him and wanted him back. There's some question, however, whether or not the writers themselves over-exaggerated the sympathetic response while downplaying the hate, as a sort of manufactured Take That towards the fans. It's been suggested that the actual fan response was much more mixed, and the negative responses were simply ignored and brushed under the carpet. In a time before the Internet gave people the opportunity to publicly voice their opinions of such things, it's hard to say. Cypher was also a perfect example of Idiot Ball . Not him - everyone else in the X-Men and New Mutants. Because he had a non-combat power, he wasn't given NEARLY as much training as the rest of the New Mutants in combat skills. If he was going to be going along with his teammates into dangerous situations, two things should have been factored in: 1 ) Give him MORE combat training, probably from Wolverine himself, to turn him into a Badass Normal , and 2 ) ARMOR, not spandex. Those few of us who actually liked the character were utterly enraged at his death.
Vibe's death in the '80s Justice League of America comics: Reviled in life, a hero in death. He asphyxiated so graphically you couldn't help but feel bad for the guy just that one time.
Steel, who died at the same time, is less remembered. Perhaps what made Vibe's death stand out more was the fact that the skinny jerk, for the first time in thirty issues suddenly showed a glimmer of true heroism. A desire to help others because it's the right thing to do. A sudden desire to be a better man. Even the dullest stone sparkles a little, if polished right. It's something J.M. De Matteis is very good at... finding the inner light in any character, no matter how rotten. Then, just to twist the knife, Vibe's murdered within moments of his epiphany! He learned his lesson... but died anyway, alone. The end! Powerful, powerful stuff. On the other hand, the only thing most people can remember about Steel's issue is the nightmarish panel where he cries out "Help-Me-Help-Me-Help-Me-Help-Me" after being shattered.
Runaways: Xavin's Heroic Sacrifice to save Karolina from the rest of her race seeking revenge against her for her parents actions. Got this reader who always hated that smug asshat.
The fate of Marvin and Wendy from Super Friends in Teen Titans #62. Yes, they were annoying. No, they did not deserve to be brutalized by Wonder Dog, who kills Marvin and leaves Wendy comatose.
In Archie Comics' Sonic the Hedgehog, occasional character Tommy Turtle was finally put out of his misery and killed off (for the second and final time) in issue #169, when he was blasted to dust by Dr. Eggman's latest weapon. They ended up erecting a tombstone (even though there was nothing left to bury; his ashes got lost in the wind), and naming a hospital after him. This is also a Heroic Sacrifice: he was infected by nanites which carried the evil AI A.D.A.M. He was able to resist the mind control just enough to fly to his death.
Quite a bit of the Harry Potter fandom was indifferent to Dobby, if they didn't find him extremely annoying. He was considered to have a low probability of dying, and nobody was expecting to be heartbroken if he did. Then Deathly Hallows came out... and it was a Tear Jerker if there ever was one.
Some fans never liked Ozzie from Avalon: Web of Magic, because he was just the useless cute mascot comic relief. And then in Dark Mage, he acknowledges his uselessness, becomes less useless, and is the Only Sane Man. And then he's killed by his best friend while trying to save her.
Inverse example from Jane Austen's Emma after Frank Churchill's manipulative, hypochondriac Aunt dies of a stoke Austen says this:
Goldsmith tells us, that when lovely woman stoops to folly, she has nothing to do but to die; and when she stoops to be disagreeable, it is equally to be recommended as a clearer of ill-fame. Mrs. Churchill, after being disliked at least twenty-five years, was now spoken of with compassionate allowances.
In Iron Fist, Castin Donn is the least sympathetic Wraith. He's kind of annoying, doesn't respect Wedge's judgments enough, and suffers from a kind of Fantastic Racism which we don't see very often - he's had so little contact with nonhumans that he's awkward and uneasy around the aliens in the squadron, and never makes the effort to desensitize himself to them. When Wedge vetoes his plan he goes ahead with it anyway, sneaking into enemy territory on his own. He might have gotten away after being seen if he hadn't been distracted by the sight of a lab where really rather gruesome experiments were being performed on nonhuman species - he went in and freed a subject, and was killed. No one on his side ever knew that his speciesist views were changing at the end.
In Tides Of War, Archmage Rhonin, generally regarded as a Mary Sue from one of the most hated licensed authors in the Warcraft Expanded Universe, was given a tragic and poignant Heroic Sacrifice expending all of his magic to prevent the mana bomb's destruction from destroying most of the world, localizing it to just Theramore city.
Live Action TV
24: Season 3, Ryan Chapelle. He shows up in 23 episodes across the first three seasons, and in 20 of them he's a Smug Snakeand an Obstructive Bureaucrat. He softens up in the 21st, just in time to find out he has to die: the villain made a deal that the heroes needed, and one of the conditions was that Chapelle be executed. Suddenly he becomes incredibly sympathetic and human (The 23rd is just his body being recovered by said villains).
Chapelle is a particularly great case because Jack asks if there's anyone he wants to contact before he dies. Chapelle says no, his only friends are at work. Considering that we've only seen him at work where he seems to be something of an in-universe Scrappy... ouch.
Lynn McGill in Season 5. Starts out as a douche, but after his sister is killed, he has a change of heart, and you can't help but feel sad for his Heroic Sacrifice (the fact that he's played by Samwise Gamgee doesn't hurt).
The page quote is about an example from Season 1, when Janet York is killed by a man pretending to be her father. That episode is when 24, a show that had been somewhat motoring along to that point, became seriously good.
The evil, vain, manipulative Sherry Palmer, who died in Season 3.
George Mason in Season 2. If not to viewers, certainly to the characters on the show.
Dina Araz. She wasn't that thrilling a villain and later very reluctant ally to Jack Bauer, and most of her arc in the first half of Day 4 took up way to much time that took away from the more interesting character in the season. But geez the way she goes out is a downer.
Dana Walsh. When she was introduced fans weren't happy with her lackluster arc about her former boyfriend trying to blackmail her. Then it was revealed she was working with the villains and opinions about her character improved a bit, but with a Broken Base at best. But then her final episode came in where she was executed in cold blood by Jack Bauer even with her begging for her life. Not only did just about everyone feel sympathy after that, it demonstrated just how far Jack had lost it on his quest for revenge in one of the very rare killings he's made where we weren't supposed to be rooting for him.
Battlestar Galactica (Reimagined): Cally's death in new show. She had her fans, but more than her share of detractors, as well. It was so affecting that Jacob, the Television Without Pity recapper who made a regular running gag of her, devoted most of his recap of that episode to a deep psychological analysis of her (then again, Jacob writes deep psychological treatises about his breakfast muffin, so take this with a grain of salt). A good summary of the fan reaction would be this.
A lot of this has to do with the way she was offed. She was nearly Driven to Suicide, talked down from it, immediately knocked unconscious by the same person who talked her down, and woke up in time to see said person holding Cally's own infant son in a maternal-looking manner. She then met Cally's gaze and gave a tiny smile before pushing the button that threw Cally out the airlock. Even for the haters, that was a bit much.
Another example is Anastasia Dualla, who started off well, but after her "relationship" with Apollo (dubbed "The Love That All of a Sudden", or - factoring in Starbuck and Anders - "The Quadrangle of Dooooom") was not very liked by the fandom. Then, in "Sometimes A Great Notion," after a nuclear war-ravaged Earth is found she, quite unexpectedly, blows her brains out after a long romantic date that gives her ex-husband (Apollo) hope that their relationship might be rekindled. It was probably a good writing decision, given that if she hadn't, what happened immediately after that series probably would have broken her spirit further.
Kat's death could be taken as a candidate with much greater demographic appeal from the same show, particularly considering what was revealed about her past in the same episode. Though some viewers liked Kat; she was the only character who would consistently and unapologetically call Starbuck on her bullshit.
Ellen Tigh, who was previously unsympathetic and disliked by much of the fanbase, got a heartwrenching death scene when her husband executes her for collaborating with the Cylons - something she did for him. The ironic thing is, both of them are Cylons, so she gets better.
And then there's the death of the entire Quorum of Twelve - the very moment they finally do something not stupid, they all get killed for it.
Blackadder: The ending scene, "Goodbyeee!", where Captain Darling, supercilious little toad that he has been, suddenly becomes very human and likable. And he dies 5 minutes later.
Buffy the Vampire Slayer: Kendra in Season 2. Sure she was an annoying character with more than a little shade of the Ethnic Scrappy, but it was still a bit of a shock to see Drusilla take her out so easily.
Burn Notice: Nate Westen. When Nate showed up in an episode, it was a given that by simply being Nate he'd completely screw things up for Mike and the gang. Then he manages to single-handedly collar the Big Bad of the series at that point - and the first time he's ever done something right, a single gunshot rings out. Even the fans who hated Nate were in tears at his last words to his big brother.
The Chaser's War On Everything: The October 17, 2007 episode featured "The Eulogy Song" sung by Andrew Hansen. It controversially cataloged a list of dead celebrities renown as "top blokes after death", embodying this trope perfectly.
Desperate Housewives: The extremely despised Nora went out with a bang. Even though it was expected and hoped for, the episode managed to make it a tragic and shocking.
Throughout the series, Edie Britt was a Love Her Or Hate Her character—you either thought she was witty and not used enough, or catty and hung around the show for way too long. Yet when she actually was killed off in season five, the people who despised her ended up mourning her death just as much as the people who loved her, especially after her tribute episode.
Dexter: Happens in Season 2 with the immolation and framing of James Doakes, especially given a few little touches to the character that fans were quite fond of (such as the voice mail message).
And as of the Season 4 finale, Rita.
Though for many, she wasn't a scrappy until the very season they killed her off. Makes you wonder if her shift in personality was done in order to annoy the audience on purpose.
Doctor Who: Believe it or not, there is a portion of the fandom that cried over Adric getting blown to bits.
It wasn't so much the actual death scene in that case, but the Silent Credits over a picture of his broken star. Beautifully touching.
Donna Noble. Though only a Scrappy in her first appearance, having developed by the time she was on for a full series, some of the fandom grew to like her and got really annoyed after she got a bridge dropped on her (death is relative).
Downton Abbey: Lady Sybil; she just seemed to be the "modern audience appeal" character, the typical Rebellious Princess that you'd find in any animated film from the '90s. However, her death after giving birth to a daughter was genuinely shocking and tragic.
However, it ought to be noted that she was /far/ from being a scrappy in the eyes of many audience members. The whole "modern audience appeal" thing actually did appeal to a large portion of the audience.
Eureka: Nathan Stark was almost universally disliked by both the characters as well as the fans, until season 3 where he sacrifices himself to save the universe.
ER: Television Without Pity frequenters are often split on the death of Lucy Knight, who, though annoying, got an incredibly good sendoff. Some were ecstatic that she was gone, under any circumstances. This story arc also had John Carter almost killed, and, since many fans were on the fence with him at that point, he garnered huge sympathy points.
Grimm: Angelina Lasser. Many fans groaned and pulled their hair at the news she, instead of Roddy, Holly, or Ariel, was going to make a return during Season Two. However, she is shot and killed while saving fan favorite, Monroe, and essentially gave her blessing for him to move on and continue his romance with Rosalee. It also gets worse when the final scene of the episode has Monroe partaking in a Blutbad burial ritual for her and once done, gives out a long and sad howl into the wilderness.
Harper's Island: Fat guy Malcom Ross. Buried his best friend's, nice-guy nerd Booth, body in the woods after he accidentally shot himself, taking the bag of money into his room and not telling anyone about it. His panicky nothings wrong attitude and sobbing when the truth comes out made him a hated character in many circles. But everyone cried when, with Roy Orbison's Running Scared playing in the background, he burns the money and is subsequently chopped, beaten and thrown in a furnace.
From the same show, violent townie Shane was probably the least likable character on the entire series. So how does he go out? Mortally wounded, single-handedly taking on the serial killer to give the heroes enough time to escape.
Heroes: Isaac had been stagnating as a character for quite a while before Sylar killed him, but his death and the scenes leading up to it were handled well enough that many viewers who had been complaining about Isaac were touched by his exit.
Niki. As much as the character was hated, her death was still sad, being that she couldn't even use her power at the time. Then Tracy showed up and all that went out the window.
House: While Season 7 was considered lackluster by many, Thirteen's reintroduction in "The Dig", which has House taking her on a road trip after she's gotten out of prison for euthanizing her brother who was dying from Huntington's, considered one of the best episodes in that season, improved opinions of her in the eyes of many.
In-universe example with Amber: Foreman admits that House's team disliked her and still would if not for her imminent death, but they're still crushed when she dies.
Joan of Arcadia: Judith Montgomery. Everybody hates this Cousin Oliver who broke up the already established group dynamic, but her death was done in such a powerfully dramatic way that some fans began to wonder why they hated her in the first place.
While we're on the subject of Lost, how about Shannon, Shannon, and more Shannon. Just when she starts becoming a compelling character and not the vapid Rich Bitch, as well as we get to learn how much her Evil Matriarch stepmother crashed her dreams... boom, shot in the stomach.
Also, Charlie, while not necessarily a Scrappy, had strong dislike from many fans, especially after his bizarre actions in the episode "Fire and Water". However, he was highly redeemed in the episode "Greatest Hits", and died very heroically in the next episode.
The Mentalist: Bosco was not popular, mainly because he kept calling Jane out on his crap and was in love with Lisbon, which pissed off the Jisbon shippers. His death, though? Genuinely moving. Made so by Lisbon.
Neighbours: Jessica Wallace, hated by many viewers and most of the other characters for breaking up Ringo and Rachel, had such a realistic and tragic death scene that producers deemed it "too convincing" and had to edit some of the most upsetting parts out.
Moody rich girl Serena Bishop suffered through attempted-rape, finding out her boyfriend was really her half-brother and a plane crash. She was eventually lost at sea.
Bridget Parker received much negative backlash from both the public and the media when she first joined the show, and many viewers called for her death. Ironically, just as fans had warmed up to her character, she was killed off in a freak car accident.
The Sarah Connor Chronicles: Riley went from becoming The Scrappy in record time to getting Rescued from the Scrappy Heap when we found out she was from the future (and thus actually served a purpose on the show besides giving John someone to suck face with); much of the fanbase mourned her death after discovering just how much her supposed savior screwed her over. Going out in a brutal fight to finally take control of her life, all in less than one season, probably helped.
Smallville: Lana Lang might be much hated by fans, but it is still sad to see Brainiac trap her in a catatonic state.
Supernatural: A lot of the fans couldn't stand Bela, yet many of them felt a staggering amount of sympathy for her in the episode where the hellhounds come to get her. It might have helped that the actress got better and less annoying in her absence.
And then there's Jo and Ellen Harvelle, the former of whom was positively reviled during her S2 days and the latter of whom was perceived to overstep her boundaries with the boys later on, and they were given one of the saddest send-offs in the show.
Torchwood: Owen's death (deaths?). That was largely helped by Tosh's own exit - well-acted and really quite heartbreaking.
True Blood: The fandom had a massive load of hate for Sam Merlotte's troubled younger brother Tommy, an illiterate, dumb, well-intended Designated Villain who was generally thought of as annoying, a nuisance, and a filler character. In the end, though, he sacrificed himself, transforming into Sam and settling a debt with the ex-husband of Sam's girlfriend, which ended up with him being bludgeoned to death. Not before he could deliver the following line, which had tons of fans that hated him crying desperately:
Ugly Betty: May have problems with annoying characters taking over the plotlines, but it has a knack for a good Montage Out, thus giving us the following examples:
It's been said that nobody cared about Bradford Meade until he was killed off.
Even the infamous Walter, though he didn't die, got a respectful and melancholy send off when he was Put on a Bus. The fact that viewers were able to feel anything but joy at that moment is a testament to this trope.
Daniel's love interest of the 3rd season, Molly, was generally considered pretty boring even when we knew she was terminally ill but the actual moment of her death was beautiful.
The Walking Dead: Lori's death. Before bleeding out, she asks Maggie to perform a cesarean on her, without taking any morphine, so that her child can live. It gets worse as her own son, Carl, has to shoot her corpse, so she doesn't reanimate.
Warehouse 13: Arguably, Agent Steve Jinks of the team fits this trope. While not a particularly disliked character, he did - before Character Development - feel like an extremely token New Guy, not helped by being background-to-absent in many episodes of his introductory season. When it's finally revealed that he's been callously killed after being discovered as an Undercover Good Guy, it's an incredibly powerful and affecting scene. Truly, nothing in his screen life became him as much as how he left it. He got better, though.
War of the Worlds: The death of Norton Drake during the second season. For the first season, Norton was a near-insufferable genius whose main job was to roll around a lab in his wheelchair and provide scientific technobabble to the main characters - and this was after the actor who played him stopped using a ridiculous Jamaican accent for the first few episodes of the series (the character did get one episode of much-needed character development in the latter half of the first season, though). In the second-season premiere, however, just as it looked like he might take on more of an active role with the Blackwood Project, Norton gets shot by a clone version of one of the main characters, gets enough strength to crawl over to a panic button and press it, then gets shot again off-screen... and then his body is blown to smithereens when the house he worked in explodes, and almost all of the characters promptly forgot about him. Norton's death is one of the main reasons why the second season is Fanon Discontinuity in the eyes of many fans.
The X-Files: Agent Jeffrey Spender, shot at point-blank range at the end of the first episode in which he developed any character beyond that of being an annoying, weasely foil to Mulder and Scully. He was eventually revealed to be Not Quite Dead, but at the time, some people were stunned he'd gone into a two-parter practically chanting "Kill the Twerp" and came out of it really upset that they'd killed the noble Spender.
Liane's death in Jeanne D Arc. She was whiny, annoying, and undeveloped, and you are forced to use her in a certain point of the game when she replaces Jeanne, which is, by the way, when she becomes an incredibly crazy (and whiny) general... but still, when she is executed by burning for crimes of 'heresy' she had nothing to do with, screaming that it wasn't her fault and thinking she was hated by her friends, you can't help but feel sorry for her.
Duke Nukem Forever used to be the butt of every joke out there. After it was officially canceled and gameplay footage was released, most people commenting on the video claimed it looked fun.
In Xenogears, Hammer the Supplier was reviled by many a fan as annoying and backstabbing, but most of that could be forgiven not only because he's gone, but because it's so obvious just how much other characters miss him, especially Rico and Elly.
In Super Paper Mario, it's revealed that Luvbi is the last Pure Heart. Nobody was really fond of her before this, but the scene is still very moving and the characters are sorry to see her go.
A huge portion of the Splinter Cell fanbase has an extreme love-hate relationship with Colonel Irving Lambert, known for his banter and his frequent decisions on when to end the mission. So when Double Agent came along and included the dilemma of whether or not to shoot Lambert as one of its selling point, more than a few stating their over-the-top-desire to finally do him in. THEN Ubisoft made Essentials, which makes shooting him necessary to complete the game, and the enthusiasm dropped like a rock. THEN Conviction came out which CONFIRMED it. God help whoever decided THAT.
Grobnar of Neverwinter Nights 2. He is mostly the annoying comic relief, but Mask of The Betrayer reveals that he had a stupidly awesome death: Attempting to save a 7 foot tall construct of solid metal by putting his squishy gnome body between it and a falling pillar.
Mask of the Betrayer does this to Casavir, too - dismissed by many players as a painfully straight take on the paladin, he sacrificed his life by holding up a collapsing ceiling so that the others could escape. Qara and Elanee also perish, but their deaths are fairly ignominious, and fall more into Take That, Scrappy!.
In Mass Effect 1, Kaidan and Ashley, your two party members, are both Scrappies for various reasons; Kaidan for his Master of None tendencies, and Ashley for her bitchy tendencies. But, Virmire, damn...
The survivor, gets even more hate from some people for refusing to work with Shepard for being affiliated with Cerberus. In Mass Effect 3, it's possible (and depending on your choices) necessary to kill the survivor, and his/her last words are quite sad.
Udina, of all people, in Mass Effect 3. Sure, he was an obnoxious ass in the first two, but here he becomes quite a bit more sympathetic in his desperation to get aid for his homeworld. Even the attempted coup seems more sad than anything. He did it for Earth.
The Legend of Zelda: Skyward Sword has Fi, who, while not universally hated, is still something of a Base Breaker due to her tendency towards being Captain Obvious. Even if you hate her, her "death", which is a Heroic Sacrifice that will take centuries, and which she prefaces by admitting feelings for Link that she was incapable of admitting until the end due to programming, is still a tear-jerker.
Alister in Tomb Raider Legend was considered to be extremely whiny and annoying while always quipping in at the most inappropriate times (lampshaded by Lara when she tells him to shut up as she tries to make some tricky acrobatics). In Underworld, Alister gets shot and killed by Lara's doppelganger, dying in Lara's arms. For an annoying sidekick, it's still damn sad to see him get killed when he isn't a fighter like Lara.
Persona 4 has an In-Universe one in Kinshiro "King Moron" Morooka, a JerkassSadist Teacher despised by his students for his asshole attitude. Despite this, the protagonists/main characters comment that he didn't deserve to die, for all he was an asshole, as Yosuke, the class slacker, expresses pity for him.
Tsukihime: Not everyone considers her a Scrappy, but for those that do: Tohno Akiha gets two different death scenes in two different story branches, and they're both uniquely heart-rending. One, she has become a mindless monster and Shiki honors his promise with her to kill her by his own hands (a Bad End). Two, she's fighting with SHIKI at the High School and lets herself be torn apart by him to protect Kohaku. She barely holds on to consciousness long enough to ask Shiki: what is he doing at his school at night? He yells it's not important, and they need to get her help, but she keeps insisting on an answer. Finally he replies it's his school, and it's not strange if he's there either in the day or at night. Akiha seems to accept this answer, realizes it was a pretty simple conclusion, and then dies (this is actually part of Hisui's True End).
It doesn't help that even Akiha's good endings are pretty screwed up.
Erika in Umineko no Naku Koro ni. While she was nothing but a (intentional) Canon Sue/Parody Sue in EP5, in EP6 she was fleshed out showing how her refusal of there being two sides of a mystery was caused by a failed romantic relationship. She seems to have understood this by the end of EP6 before dying after her duel with Beatrice.
She deserved to die because she capped off her role as The Scrappy by Jumping Off the Slippery Slope, killing the Cool Old Guy, weakening the fabric of the universe, and ensuring that the villains won the battle for Azure City, all while thinking she was still doing the right thing.
She becomes sympathetic in the eyes of the audience because her last actions were made under the belief that she was saving everyone instead of dooming her side to exile, and then after being mortally wounded as a result, the spirit of the founder of her order explains to her just how she screwed up and tells her that she won't get a chance at true redemption, but that her celestial horse will still get to visit her in the afterlife. * Sniff* And in a 'verse where it has been proven that Death Is Cheap, she was decided by the author to be so unworthy of resurrection and redemption that any chance of it happening is rendered moot in a throwaway gag.
Not to drive the point home, but another aspect of the death that turns it into a touching moment is her last words. Miko was, above all else, uncompromising. She would never accept anything but the most pristine of Lawful Good, would go over the top with her expectations and would scream and cry whenever she did not get her way. Yet here, in her last moments, she was denied the thing she wanted the most, being a paladin. When that happens, she shows a final bit of character development when instead of crying about it, she instead just asks if she will see her only real companion again. And when given just that small favor, instead of screaming about what she really wanted, showed maturity in compromising for that one little bit, by saying "I can live with that." In her last moments she learns to compromise what she wants.
Some think she might just have been driven a tiny bit insane by the revelation that said cool old guy mentor and father figure who personally recruited her into the order of paladins had been lying and manipulating her (for the great good but still that has to be like finding out your prudish judgmental grand mother has a hot 18 year old boy toy.) resulting in her paranoid delusions but this party is just less vocal about their opinion. Also the fact that the party magnificent bastard (Belkar) was deliberately pushing all her buttons the moment she arrested the party.
Tsukiko gets her own one later on. After parodying the Mary Sue a bit too closely (polychromatic eyes, dark, mysterious, and misunderstood, yet beautiful, etc), her death scene when she crosses Redcloak is actually pretty touching. She has the life drained out of her by the very undead that she so cared for (magically controlled by Redcloak), whispering "Why don't ... you love ... me?" with her last words.
Terry's death in Blip. Up until then, most of the fans had hated her for breaking up K and Bishop, but when she died, they lost it. It helps that her death scene was a straight-up Tear Jerker.
College Roomies From Hell had this coming from Dave. It failed spectacularly, because no one realised that Dave was meant to be The Scrappy. Quite the contrary, he became one of the most popular characters, so the author had no choice but to bring him back and actually make him a protagonist.
The outpouring of grief that followed the sudden death of WrestleCrap Radio's robot sidekick Johnny 6 during the April 25th Podcast, after Crappers had been clamouring for his destruction for weeks.
The death of Liam Black in Survival of the Fittest version 3 was considered by some members to be well-written, and genuinely saddening, in spite of the fact that the character was extremely unpopular whilst alive.
Red in There Will Be Brawl was disliked by some fans due to his naive and cheerful personality in a World Half Empty, and suspected by many to be the butcher (especially in regards to that Jigglypuff he was subtly hiding from Luigi). Then... "So, uh... was I any good?" Turns out he was training the Jigglypuff to sing for Luigi. Thankfully, Leaf uses it to finish off Wario, who killed him.
Spencer D. Bum in The Spoony Experiment was considered a Scrappy by some of the fans, even though he only appeared 2 times. Then his heart was ripped out of his chest onscreen by Black Lantern Spoony.
Played with on the very last episode of the (original) Beavis And Butthead series, "Beavis and Butthead Are Dead." (They literally "call in dead" because they don't feel like going to school that day.) Most of the people at school - both students and faculty - subvert the trope in that they are at best apathetic, but Mr. Van Driessen actually cries over their "deaths." Of course, this may not be the best example since Mr. Van Driessen was an Extreme Doormat who tolerated the boys' misbehavior to an absurd degree.
In Adventure Time, both of the Earls of Lemongrab are both extremely annoying and unpleasant characters. However, in the episode "Another Five More Short Graybles," the first Lemongrab apparently ate the second Lemongrab alive, appearing to have killed him. This segment of the episode ends on a massive cliffhanger as Lemongrab 2's fate is left ambiguous. Although both of them are seen as scrappies by fans for being extremely annoying, stupid, rude, and insane, most fans at the present time are worried sick about Lemongrab 2. The ones who believe that he is dead are actually sad that he apparently died in such an awful way, and the ones who still harbor hope for his life are sincerely wishing for his safe recovery.
The entire Adventure Time fanbase cried in unison when Lemongrab 2 actually died.
In the Transformers Prime episode, "Rock Bottom," Miko almost got this. Long reviled for her tendency to charge after the Autobots into the line of fire, jeopardizing the mission and sometimes many lives, in this episode she's simply allowed to accompany them into a mine they think is safe. Then Megatron and Starscream happen upon the mine, causing large sections to cave in. Bulkhead saves Miko by holding up the portion of the cave ceiling just above her, but this means he can't move. Demonstrating impressive strength, Miko begins yanking up the large boulders blocking the tunnel and throwing them aside, in a nonetheless vain attempt to save Bulkhead that nearly kills her from asphyxiation. Even when Jack conveniently barges in with a boring machine and rescues Miko, now all-but dead, she's horrified to leave Bulkhead to his fate. He is later rescued, too, so everything ends up okay, but it's still probably the decisive moment when Miko begins to get Rescued from the Scrappy Heap.
In the Exosquad series there are several notable examples, but the most Prominent was the much hated Captian Matthew Marcus. Not only was he lacking of strategic skills, had sheer arrogance, sported a hair-trigger temper, and tyrannical in that he charged the first officer to question his dangerous orders as a mutineer, but he practically single-handedly crippled the Exo-Fleet. Not only was that humanity's greatest hope in winning the war and saving their species, but did so after going to mutiny, creating a coup, and sending the best combat squad on a dangerous and meaningless mission. Despite all this, he had an incredible send off in that he refused to give up the fight, attempting to redeem his failures and actions. When a protagonist was sent in to rescue him he refused to leave, forcing him to leave at gun point and going for a heroic sacrifice, taking out a number of enemy ships and buying some time for the survivors of the fleet he destroyed to escape. His last words were to be relayed to the Admiral he betrayed: "Tell him that Matthew Marcus knew how to die!"
Somewhat subverted that despite the impact and incredibly well done death being very memorable. He was never really missed by fans, also, that last scene as he has the Exo-Carrier self destruct in enemy lines has his face showing a less heroic expression, but more of a crazed suicidal rump of joy!
Family Guy: Brian was loathed by many for being a preachy Author Avatar the past few seasons, but people still felt bad when he died in "Life of Brian".