Code Geass pulls this rather surprisingly with both of Lelouch's parents, Emperor Charles (whom he despised) and Empress Marianne (whom he revered); the two formed a plan to change the world for the better shortly after they met, and since Lelouch and his sister Nunnally were their favorites, they intended to let the kids in on it when they were old enough. However, they didn't bother taking into account how the kids would feel about forcibly changing the nature of all of humanity. And all this is before you throw in their Evil Plan to protect the kids which resulted in both kids being mentally and emotionally scarred, and drove Lelouch to try to kill his father in the first place.
Lampshaded in the audio commentary for the episode in which the parents' Templar-hood is revealed, when the episode's director comments "They probably thought they were doing the right thing, but Lelouch wanted to say that they weren't Good Parents. We wanted to make sure that was clear."
Recent chapters of Tsubasa Reservoir Chronicle suggest that Syaoran and Sakura Li went path for their son, [male] Tsubasa. Their moves include getting sealed in separate parts of a glass container for the better part of their offspring's lives as a payment for his safety, Sakura sacrificing a Magic Wand she was given by an alternate universe version of herself so [male] Tsubasa can go to an alternate dimension to help [female] Tsubasa, his love interest, and then facing the Big Bad in a battle that potentially can destroy the multiverse in an AWESOME Big Damn Heroes moment. All this because [male] Tsubasa fell in Love at First Sight with the person his mother was cloned from.
A minor suspect in an early Detective Conan story locked her own son Akio in the basement of her house for six years so the Statute of Limitations would run out on Akio's accidental murder of his apparently abusive father... even when Akio did aknowledge his guilt and wanted to pay for his crime, and being locked downstairs only made him cross the Despair Event Horizon. Ultimately, Conan and the Detective Boys found out as they sneaked in the apparently abandoned house; Conan uncovered the mother, helped Akio convince her to let him go, and they turned themselves in together.
Giovanni from Pokémon Special. Wanna find your missing son? Simple, just destroy the Sevii Islands, put other families through hell, nearly kill quite a few people, and put the protagonist through a whole lotta traumatizing shit, etc..
Whitebeard of One Piece is an example of this to his "sons," as he considers killing a crewmate to be an unforgivable crime. When Ace, who had gone after Blackbeard for killing his division commander, lost to Blackbeard and was turned over to the World Government, Whitebeard sent his entire fleet of pirates to Marineford to save him, playing into the World Government's plans as well as Blackbeard's.
This being Whitebeard however, he was playing a hefty case of Xanatos Speed Chess with the World Government during the encounter and his defeat and demise happened because of unforeseen events such as Blackbeard turning up and Ace being killed, resulting in a Heroic BSOD.
Despite typically being cold and dismissive toward his daughter Hinata, Hiashi Hyuga of Naruto has some hallmarks of this, like when he activated his brother's curse seal merely because he sensed that he was considering harming Hinata.
Berserk: The King of Midland practically destroyed his own kingdom just to make Griffith's life a living hell after he deflowered his precious daughter, Princess Charlotte who he later tried to rape and evidently fell deeper and deeper into insanity afterward.
The Count can also count, since he was so determined to keep his daughter Theresia away from the evils of the world himself being one of them that he locked her in her room for most of her life.
Suits Renton and Eureka to the T in Eureka Seven Ao for their goal to ensure their son Ao's survival after the tragedy that happened to their firstborn daughter.
The twelve members of the Pride in Runaways are promised six places in a coming paradise. In order to avert infighting about who gets the honor, each of the six couples agrees to grant a spot to their children. Of course, earning these six places involves routine human sacrifice and taking over the world....
Don't forget how Geoffrey Wilder from the 1980s bargained with the Gibborim in the present - just because he wanted his to-be-deceased wife and son back (keep in mind that at this time, Geoffrey hasn't even met Alex yet. He also chooses Nico as the sacrifice just because she refused the advances of Alex. Oh, and there's also the time when the kids are stuck in 1800s New York and Chase meets the past versions of the Yorkes, who were also time traveling in that date. Upon learning from Chase that their daughter is going to die in the future, Mr. Yorkes tries to attack him. The pair immediately begin making plans to keep Gertrude safe - and bring a nuclear bomb from the future to blow up 1800s New York. As revenge for Getrude dying in any possible future.
Mr.Chau from Scott Pilgrim. Once he finds out his daughter, Knives, is dating a 23-year old white boy (or used to at this point) he did the most logical thing possible... He went around with his ceremonial sword and hunted Scott so he could decapitate him. This eventually helped Scott though as he used Mr.Chau as a distraction in a battle with one of Ramona's evil exes and, after that, made peace with him.
Some adaptations of the Fairy Tale "Rapunzel" portray the witch this way, possibly to make her seem more sympathetic. Included among them are the Donna Jo Napoli's novel Zel and Stephen Sondheim's musical Into the Woods. In both those versions, the witch truly loved Rapunzel and was trying to protect her.
In the Naruto fanfic A Father's Wrath, instead of the yondaime, Naruto's father is Orochimaru. He's so enraged by Naruto being made into a jinchuriki, that in this continuity it's his primary motive for forming the sound village and attempting to destroy Konoha. In sound, he also makes Tayuya something akin to a slave for Naruto for slapping him. It's implied he would have had her killed if Naruto hadn't spoken up about being in a panic at the time and that she'd been trying to calm him down. Otherwise, however, he seems to be a just ruler, and a devoted parent.
In The Immortal Game, Esteem claims that everything he did to Rarity — Training from Hell, emotional (and possibly physical) abuse, killing her mother (who opposed his plans) — was all for her own good, to make her strong enough to survive and rule by his side in the new order he'd help Titan create. side note
He also nearly cut out Prince Blueblood's tongue for how he treated her; he's a real piece of work.
She calls him out on this during their confrontation, and disowns him.
Christof in The Truman Show takes this to the extent of trapping his adoptive son Truman in an entire "perfect" fake world, with actors playing every person in Truman's life, so that Truman will never be exposed to the evils of real life.
At least this is what he claims. The fact that he then TELEVISES this as "the ultimate reality show" rather makes that doubtful as his real motive. He even instills a phobia of flying or sailing in Truman to keep him from finding out he's in a huge dome.
The Positively True Adventures of the Texas Cheerleader-Murdering Mom is based on a true story about a woman who plotted to kill her daughter's cheerleading rival.
Anakin Skywalker of Star Wars. Heartbroken by the seemingly impending death of his wife and possibly of his child (whose future he cannot see in his visions), he goes on a savage killing spree to to immerse himself in the powers of the Dark Side of the Force, in order to gain the power to save Padme Amidala and, if need be, the baby too. (Note that this is not precisely clear in the movies - the novelization makes it much more apparent.)
Viktor in the Underworld series, to the point where the entire Vampire-Lycan War began due to his being so much of one that he had his daughter, Sonja, executed after finding out she was pregnant with the child of a Lycan. Naturally, when several centuries later he discovered his adoptive daughter, Selene, had begun to consort with a Lycan, he doesn't take it well.
In Easter Bunny, Kill! Kill!, the killer who's been taking out Remington's low-life friends out to be Nick's seemingly-oblivious mother, Mindy.
Liam Neeson's character of Bryan Mills in Taken fits this trope to a T. All in the name of rescuing his daughter, he is not afraid to kill whoever stands in his way, or even torture those who can give him advice as to where he can find her.
Adam Hauptman of the Mercy Thompson novels can be like this with his teenage daughter, Jesse. When Jesse is beat up at school because her father is a werewolf, she refuses to tell her father who it was, because if he knew, he would kill them.
Queen Cersei Lannister in A Song of Ice and Fire; she is terrified that something will happen to her children (not an unjustified fear, given they're born of incest with her brother and are thus treason to her royal husband) and protecting them is a large part of her motivation in some of the most immoral acts in her regency. It's easily her most favorable attribute.
Played with in The Count of Monte-Cristo: Madame de Villefort will go to any lengths to ensure that her son inherits a large fortune; which includes poisoning nearly every member of her family, including her step-daughter
Sara in My Sister's Keeper. Sara had a child (Anna) specifically so it would be a perfect tissue match for her middle daughter Kate, who has severe leukemia. She also neglects her older son Jesse once it is found out he is not a genetic match for Kate. After Kate's kidneys fail, Sara and her husband want to use Anna's kidneys. Anna deciding, she's had enough and sues them for medical emancipation. With Kate's blessing.
Harry Dresden himself in Changes. The Red Court took his daughter, and he will do whatever it takes to get her back. Including becoming the Winter Knight and causing the genocide of the entire Red Court.
It goes beyond that. He mentions to Mab that if she didn't take him up on his request, he'd be willing to take up Lasciel's coin and join the Denarians, an organization of fallen angel-possessed immortals whose goal is to literally cause as much suffering to humanity as a whole as possible. And if that failed, he'd summon a Darkhallow, murdering hundreds of thousands and becoming, basically, a god. All of this, just to ensure his daughter's safety.
Harry Potter features a clever heroic inversion with Narcissa Malfoy. She is willing to betray her sworn master Lord Voldemort just to protect Draco, up to the point of hiding the fact that Harry was not killed by Voldemort as he thought.
It also includes a more traditional version with Molly Weasley: the otherwise soft hearted and kind mother kills Bellatrix Lestrange. This counts as more than just Mama Bear in part because it's the only recorded killing curse ever used by someone other than a bad guy in the books. Doubly surprising considering how strong and experienced her opponent was, but works as an in-universe version of the mythical mother lifting a car off her child. "Not my daughter you bitch!"
Dogtooth takes this trope and runs with it: both parents keep their kids in the confines of their estate, crafting images of the world outside as highly dangerous and suspicious. This leads to their portraying cats as "the most dangerous animal of all," for example.
Angela Petrelli. She even said at one point that her generation "mortgaged their souls" for the current heroes' generation. Her most obvious manifestation of this would be that she has tried to make her eldest son President by blowing up New York City.
To elaborate, in the course of protecting his daughter, Jack has tortured and killed people, faked people's deaths, played multiple simultaneous games of Gambit Roulette, shot his own wife in the head when he'd thought she'd put a contract out on Sydney, counter-brainwashed Sydney to resist programming, endured radiation poisoning, and eventually sacrificed his own life. Never, ever, find yourself so much as threatening his daughter. It will not end well.
Irina reaches this status as well, for villainous reasons. She uses both her daughters as nothing more than pawns in her endgame, but god help you if you attempt to interfere with that plan.
Lost: Ben is so worried Alex will get pregnant (which on the island is a death sentence) that he jails her boyfriend and then orders him brainwashed in a Clockwork Orange fashion. Michael is also willing to pull a Face Heel Turn to get him and Walt off the island.
Gibbs from NCIS might not be a biological father of anyone on his team, but he plays the role of Team Dad often enough (and well enough) to generally count here. Heaven help you if you hurt one of his agents - especially Abby.
A fact that Team Gibbs is fully aware of, as Abby proved in one episode when he asked why she hadn't told him about her crazy stalker ex:
Abby: Because, I wanted him restrained...not bludgeoned to death with a baseball bat.
Yoo Won Gook in Vampire Prosecutor kills any one who so much as ''hint'' at harming his daughter, Jung In. The fact that she's a prosecutor working hard to arrest him complicates matters. To this end, he even distances himself from her so that she won't be implicated when he is indicted.
Jung In: Heís the bad guy. Heís someone I have to lock away. But when the reason he did those bad things is because of me, I canít call him the bad guy. I canít even hate him.
Once Upon a Time: While Emma occasionally slides into this, Rumplestilskin is a definite, absolute example of this. He gains dark magic to save his son from going to war, and then afterwards repeatedly uses those powers unnecessarily when anything remotely bad ever happens to the boy afterwards.
In season two, Belle's father becomes this when he tries to forcibly remove all of her memories of the Enchanted Forest just because he wants to get her away from Gold. He has good reason not to approve, but his methods aren't exactly reasonable.
Queen Dowager Almedha from Fire Emblem Tellius is so determined to save her son Pelleas's life, that she's willing to let the kingdom of Daein be destroyed if that's the key to undo Pelleas's Deal with the Devil. More ironic if we see that Pelleas is not her child. Soren is.
Raphael from the Soul Series has repeatedly tried to claim an incredibly evil sword on behalf of his adopted daughter, Amy. One time, it was to try give it to a country he hated so it's leaders would kill each other because of it. The other was so he could destroy an artifact that was curing people of the vampirism he was infecting them with so she wouldn't feel left out, having contracted vampirism from him as a result of his last attempt to get the sword. As Amy is an EmotionlessElegant Gothic Lolita we have no idea how she feels about his insane plots.
Apparently she just doesn't take him seriously at all, given that in her ending sequence of Soul Calibur 4's story mode after Raphael claims Soul Calibur to create a new world for her... she pushes him into a pit during the requisite Evil Laugh.
With the obligatory "RING OUT" announcement as well.
In Borderlands 2, Handsome Jack himself. Late in the game, Angel is begging you to kill her, and he is screaming at her to stop, saying that all the bandits he's killed and people he's manipulated and the world of pure order he's trying to establish is to protect her. Keep in mind that by this point, Angel has spent most of her life imprisoned due to her Siren powers and used as a biological computer by her father, and has spent the last five years being used as a living catalyst to charge the Vault Key with Eridium, so her father's pleas sound hollow to everyone but himself and his extremely twisted viewpoint.
The Order of the Stick pulls this one off in spectacular fashion: in comic #639, after dealing with an Ancient Black Dragon who showed up to avenge her son in a brutal fashion, Vaarsuvius uses the spell Familicide on her, which kills not only her family, but the family members of her other family members, and so on ad infinitum. The page quote comes from the follow-up comic (and, it's worth pointing out, is directed towards the victim's severed head, reanimated solely for the purpose of delivering this monologue). V estimates that s/he killed a whole quarter of the black dragon population in the OotS universe. However, Karma lines up to give the perpetrator a kicking. The power required to do it was acquired via a Deal with the Devil, so V's soul is pledged to three separate Fiends, and it's further revealed that included among the bloodline was the family of Girard Draketooth, one of the legendary heroes who guards the gates imprisoning the Snarl. Perhaps most notably concerning this trope, though, V's mate is so appalled at what s/he did that they file for divorce.
Parodied quite a few times on South Park. To give just a few examples, in "Child Abduction Is Not Funny", after misinterpreting statistics that show most children are abducted by their parents, the parents of South Park end up banishing the kids from town to protect them from being abducted. In "My Future Self and Me", they pay actors to pretend to be washed-up loser versions of their kids from the future in order to scare them straight. And let's not forget the many things Kyle's mom Sheila has done to "protect" the children of South Park, like the war with Canada and the public execution of Terrance and Phillip in South Park: Bigger, Longer & Uncut.
While not strictly their father, Charles Offdensen of Metalocalypse is definitely the closest thing most of the band has to one, even if they don't realize it and generally misinterpret his presence in the Dethklok organization at all. He's also personally responsible for the utter ruin of everything that threatens the band in any way; the show's main antagonists are the threats he hasn't been able to find yet.
In the episode "Over The Edge" in Batman The Animated Series, Jim Gordon of all people loses it when Batgirl is killed and goes on a rampage to hunt down Batman (who he blames) in vengeance. He is even willing to release Bane if it will help him capture Batman. Fortunately, it was All Just a Dream.
In Hotel Transylvania, Dracula is fiercely protective of his daughter Mavis due to his promise to his dead wife that he'll protect her no matter what. He tries to instill within her his fear and hatred of humanity and built a massive hotel for monsters as a safe haven for her. He even builds a fake human village with his zombie minions playing a human mob (complete with torches and pitchforks) so that his daughter loses her wanderlust.
Tom Carder, the CAP Alert man is an excellent (real-life) example of this trope, if you're to believe that he searched his kids' electric sockets to try to find satanic symbols.
Real life example: Christophe Fauviau, who doped the drinks of at least 27 tennis players due to face his son and daughter. After one match, one of these opponents passed out at the wheel of his car due to the medication he had been slipped. He was killed in the ensuing accident.