In Fullmetal Alchemist, the main villain, 'Father,' self-identified as Van Hohenheim's son back before he got godlike powers, and seems to have had a love-hate relationship with Hohenheim. For his part, Hohenheim had no idea about the hate until the Homunculus tricked the emperor into killing his entire country and funneling their souls into it, giving it the power to create a body. It shares half the souls with Hohenheim, then revels in his horror at his entire country being a Doomed Hometown and his new catchphrase. The next time they meet, they are enemies, with Hohenheim as the Big Good, and his son, mentor, Evil Counterpart, and creator as the Big Bad.
Incidentally, this means that in the 2003 anime Envy turns out to be Ed's older brother, and in the manga it, and all the other Homunculi, turn out to be his nephews and niece.
In Soul Eater, Shinigami and his eldest son Asura. Subverted as Asura is technically a fragment of Shinigami's soul, but it still counts. Kid is not amused with this development.
In Death Note, Villain Protagonist Light Yagami is a mass murderer, and his father Soichiro is the police chief trying to stop him. However, Soichiro is unaware of his son's secret life, and he dies believing that his son is innocent.
Fairy Tail: After being excommunicated from Fairy Tail for unspecified reasons, the guild master's son, Ivan, forms his own guild called Raven Tail. They exists almost entirely to antagonize Fairy Tail.
America: At least I don't have to eat your sconesanymore.
England: (furious) Those scones were a recipe passed down from my Mumsie!
Stryfe, from Cable, is an odd example, being a clone of Cyclops' son, Cable, who was captured and raised by a future version of Apocalypse to be his son and heir. Ultimately rebelling, Stryfe seeks to slay both Cable and Cyclops and Apocalypse, whom he regards respectively as his biological and spiritual parents. He has repeatedly clashed with all of them in pursuit of his insane agenda.
Continuing this trend, Stryfe later captured Cable's son by Aliya Summers, TylerDayspring, In fact it's heavily implied i.e. all but said, that Tyler is in fact Stryfe's son due to the time when he pretended to be his Cable (nobody realized the two were physically identical for years because Stryfe was never seen unmasked by anybody else until they both came to the 20th century) and tricked Aliya into having sex with him and raised him to hate his father. As one of Stryfe's soldiers, Tyler attempted to murder Cable's friend, Dawnsilk, and was shot by his father for his efforts. Tyler's hatred for Cable turned personal after this, and he travelled back to the past, adopting the identities of "Mister Tolliver" and "Genesis". He forced his father's team, Six-Pack, into conflict with Stryfe, leading them to disband, attempted to infiltrate and subvert X-Force, which Cable was leading, and again confronted his father when the latter was possessed by Stryfe, an altercation which led to Stryfe's "death" and left Cable very traumatised. Tyler later declared himself Apocalypse's heir and was killed by Wolverine; his ghost meets with Cable during a near-death experience and the two seem to have reconciled.
Then there's Cyclops' brother, Vulcan who tries to kill their father, Corsair right after meeting him.
Obsidian, the son of Green Lantern Alan Scott and supervillainess Thorn, seems to have inherited his mother's disposition towards mental instability. Initially a superhero, Obsidian suffered a mental breakdown and turned to evil under the influence of IanKarkull, from whom his powers were derived. During this time, he attacked his father's team, the Justice Society of America, blaming Scott for abandoning him to be raised in an abusive foster home; he was defeated, fittingly enough, when his alcoholic foster father sacrificed himself to save Scott. He later allied with Eclipso and The Dark LordMordru in an attempt to plunge the entire world into darkness; Scott confronted his deranged son during this battle, defeated him, and was ultimately able to cure him of his madness.
Tom Strong's son Albrecht Strong, who his evil Nazi villainess Ingrid Weiss conceived (after what may well have been a rape) and raised without his consent. Their main antagonistic relationship is shown in a Flash Forward to 2050; as a would-be world-conqueror and a Nazi to boot, Albrecht repeatedly clashes with his Science Hero father.
Incredible Hulk: Hulk had issues with his son, Skaar, who came to Earth and waited around for Bruce Banner to return to being the Hulk so he could kill him. He eventually mellowed and got along with his father. His other son, Hiro-Kala, hates Bruce and the Hulk, and tried to wipe out Earth in his rage, using brainwashed slaves to do his dirty work; it takes Bruce and Skaar to take him down.
David Haller, aka Legion, is the son of X-Men founder Charles Xavier and Holocaust survivor Gabrielle Haller. He's also a deeply disturbed young man with vast psionic powers and multiple personality disorder, including an alt that is modelled on a crazed terrorist who tried to kidnap him as a child. Institutionalised as a child, David eventually broke out, clashing frequently with both the X-Men and the New Mutants, both of whom were led by Xavier. David eventually integrated his personalities and tried to redeem himself, but this only created worse problems, as his attempted assassination of Magneto in the past resulted in Xavier's death and the creation of the Age of Apocalypse timeline. David was briefly killed by Bishop following this. He's since turned up alive, trying to find peace in a Tibetan monastery, which he accidentally destroyed when he learned of his father's death.
Xavier's ex, Moira McTaggart, has had her own problems with her son, Kevin, alias Proteus. Conceived when Moira's estranged husband Joe raped her, Kevin was born with Reality Warper and Demonic Possession abilities, and severe emotional problems, and was imprisoned by his mother. Kevin broke out when his cell was damaged, and went on a rampage, during which he killed several people (including his father), tried to kill his mother and the X-Men, and was seemingly killed by Colossus. Since then, he has infrequently returned to attack the X-Men and Moira, who he blames for his problems. The Ultimate version of Proteus, by the way, is a Composite Character of Proteus and Legion, being Xavier and Moira's son.
In Ultimate Marvel, Captain America's Archenemy The Red Skull, is his son by Gail Richards. Growing up on a military base following his father's apparent death, the Skull hid his resentment of Cap until he was 17; he then snapped, killed upwards of two hundred people on the base, and, in a final act of rebellion against his father, mutilated his own faceby skinning it. He would go on to become a hiredassassin, undertaking numerous missions for terror groups like AIM—including assassinating JFK—before coming up against the resurrected Captain America after being hired to steal the Cosmic Cube. The battle between father and son left numerous people dead, and ultimately ended in the Skull's death, after he was hospitilised by Cap and then killed by the mother of one of his victims.
Marvel Comics really likes this trope: there's also Hyperstorm, the possible-future son of Franklin Richards and Rachel Summers, who travelled to the present to destroy the Fantastic Four, an act that might very well have prevented his own birth. At one point in the MC-2 verse he even went after his father, Franklin, ignoring the potential grandfather paradox.
In one run of Detective Comics, Batman had to deal with the psychopathic James Gordon Jr, the Commissioner's son.
Some Spider-Man comics portray the relationship between the original Venom (a delusional Type V Anti-Hero who only targets Spider-Man) and his symbiote's offspring, Carnage (an Ax-CrazySerial Killer and indiscriminate mass-murderer) this way, complete with Carnage referring to Venom as dad. His appearance was one of the few things that was all but guaranteed to force an Enemy Mine between archenemies Venom and Spider-Man.
In Beowulf, the dragon that Beowulf faces at the end is actually his bastard son by Grendel's mother.
Excalibur takes the "Mordred is Arthur's bastard" version of the story and runs with it, playing Mordred as a half-crazed Bastard Bastard who wants his father's throne, sword, and power, but rejects his love, ultimately leading to a very messy Mutual Kill.
TRON: Legacy: from a certain point of view, Clu 2.0 was just as much Kevin Flynn's son as Sam was. A combination of jealousy, poorly-worded directives, and just plain malice turned him into who we see in the present-day.
In the original The Omen, as well as its 2006 remake, the protagonist is a father who comes to realize that his son is the Antichrist.
The Big Bad of Kung Fu Panda is Tai Lung (a snow leopard), the adopted son of Master Shifu (a red panda).
In Blood Diamond, Solomon's son Dia is brainwashed into joining the local militia. Solomon pulls him back from the brink.
Shingen Yashida to his far more benign father Ichiro in The Wolverine. Which is promptly subverted later on, as desperation to avoid death made his father cease to be benign.
In Death Wish, the fourth book in the Cal Leandros series, Promise Nottinger's daughter, Cherish, is one of these, deliberately manipulating her mother, as well as Niko and Cal, for her own selfish ends, while continuing to prey on humans and sleep with her mom's ex, Seamus. She is ultimately disowned by Promise and killed by Niko, after an incident where she convinced him that his brother, Cal, was dead, in order to send him on a Roaring Rampage of Revenge against one of her enemies.
In The Quest for Saint Camber, Prince Nigel Haldane's eldest son, Conall, is this, going so far as attacking his father with magic and allowing everyone to think Nigel simply had a stroke.
Breezepelt in Warrior Cats: Power of Three and Omen of the Stars. He's the son of Crowfeather, but he allies himself with the ghosts of the villains in an attempt to overthrow the society of the characters.
Yellowfang's son Brokenstar is one of the first villains to be shown in the entire series. In fact, he was so evil that Yellowfang had to kill him to save ThunderClan.
The Chronoliths: AdamMills is the son of secondary protagonist Ashlee Mills, and is therefore protagonist Scott Warden's stepson. He's also a pure psychopath with no conscience, delusions of grandeur, and an unshakeable faith in Kuin, a mysterious conqueror who will supposedly Take Over the World at some point in the future (it is hinted that Adam believes himself to be Kuin). Born with his brain chemistry out of whack, Adam has no problem torturing his mother for information, having his stepsister gangraped for the hell of it, and attempting to murder his stepfather, all in the name of his crazed religious agenda.
Seeker Bears: Nanuluk the pizzly bear is this to his saintly parents, killing his father and trying to murder his mother (both allies of the heroes).
In Mercedes Lackey and Andre Norton's The Halfblood Chronicles, the dragon Mya is this to her mother Alara. Alara is one of the kindest dragons in the setting, adopting the half-human, half-elf baby Lashana and eventually helping with Lashana's rebellion against the elven lords. Mya is lazy, vain, and a bully who views all non-dragons (and even many other dragons) as nothing more than playthings.
Angel: courtesy of a kidnapping by murderousvampirehunterHoltz and a subsequent stay in the hellish dimension of Quor-Toth, Angel's son Connor goes from baby to emotionally-stunted, angry eighteen year old in the space of a few weeks, and carries a correspondingly huge grudge against his father, whom he blames for his situation and Holtz's murder (actually a frame job/suicide). He tries to kill Angel several times, even going so far as to trap the vampire in a steel box and sink him to the bottom of the ocean. He eventually pulls a Heel-Face Turn, but it's not until he's had his memories wiped (at Angel's request) that he is able to let go of his anger and find something approaching a normal life.
Later in the series, Connor's memories are restored to give him back the levels of Badass he needs to defeat the demon he was destined to slay. This time around he is emotionally mature enough to appreciate what Angel did for him and goes on to be a powerful ally.
Morgana on Merlin after she found out Uther had lied to her for years about Gorlois being her father when in fact Uther himself was her father. After that, she wanted him dead, no matter what.
Andrew Van De Kamp started out like this in Desperate Housewives towards his mother. It is revealed that he has somewhat of a Freudian Excuse in the second season, as one flashback shows Bree calling his much younger self a criminal and forcing him to memorize a Bree-serving apology after he swipes a lawn ornament from Mary Alice's yard out of curiosity.
Brenda Mensah to the father who abandoned her, Fred Ade-Williams in Tinsel.
The Season 2 storyline of the American Being Human features Aiden forced to confront a vampire "son" he exiled almost a century ago. Aiden hopes to find a way to reconcile and help his son return to vampire society, but his hallucination of his own sire (whom Aiden killed in the season 1 finale) warns him about this trope. He even predicts that the son will always kill the father in such a conflict because, while a son might grow to hate his father, the father will always love the son he chose and created and never be able to choose to destroy him.
All My Children: When Kendall, Erica Kane's long-lost daughter was first introduced, she quickly gained a reputation as "the most terrible daughter on daytime."
Heather Dale's "Mordred's Lullabye" focuses around Evil MatriarchMorgana Le Fay's attempts at turning her son, Mordred, into one of these. She reminds him that his father (her brother!) is a thief and a traitor who has taken what is rightfully theirs, and that he, Mordred, is to die gaining them their revenge.
Mythology and Religion
In some versions of the King Arthur mythos, the treacherous Mordred is Arthur's son as well as his nephew. This never ends well. In fact, that final battle is one of the older parts of the Arthur legend. Before his and Merlin's stories fused, long before Gwenhwyfar and round tables and lake ladies and his having any particular knights, there's a record of that battle.
In Greek Mythology, Zeus worries that his and Metis' son will overthrow him, as he overthrew his father (who overthrew his own father) before him. Fortunately for Zeus, they had a daughter (Athena) instead.
Older Than Feudalism: In The Bible, King David's son, Absalom, murdered his half-brother Amnon at a feast to which he had invited all of King David's sons. This was rather understandable, as Amnon had had raped Absalom's full sister, Tamar. David eventually forgave Absalom...but all was not well. Absalom built up support in Jerusalem, promising justice for all, and showing a humility that his father never did. With all of Israel and Judah behind him, he revolted against David and seized the city, driving David beyond the Jordan River. He ruled for years as regent, eventually declared himself king, and was slain by his father's Number Two, Joab, in the Battle of Ephraim Wood. David, despite everything Absalom had done to him, wept for his death afterward. A lovely combination of this trope, The Evil Prince, and Bitch in Sheep's Clothing.
Would God that I could die for thee, o Absalom!
Dahak the dragon god of treachery and evil is this towards his father, dragon creator god Apsu the Waybringer in Pathfinder. Running on hatred, Dahak hopes to destroy everything his father has built and targets his creations for the sheer pleasure of ruining them.
Warhammer 40,000: Horus, the favored son of the God Emperor of Mankind, was also the first to fall to Chaos. Half his brothers fell too, whether through manipulation or already being antagonistic, the result being the utter clusterfrak that is the Horus Heresy.
In Mass Effect 2, Samara's loyalty quest involves her evil progeny Morinth.
Sirrus and Achenar in Myst, to Atrus. They're ultimately enemies to everyone, including each other.
Tekken 5: Heihachi's father Jinpachi comes into play, showing himself to be an upstanding and kindhearted individual, unlike his son. Unfortunately, Heihachi challenged him for control of the Mishima Zaibatsu, imprisoned him under Hon-Maru, and left him there for over forty years (and forgot about it), leading to Jinpachi dying and subsequently being revived by a demon that now controls his body. Heihachi's own progeny, biological and adopted, all hate his guts for very good reasons. Heihachi's grandson Jin Kazama also hates him, to the point that he uses his mother's surname instead of the Mishima name and un-learned the fighting style Heihachi taught him in favor of traditional Karate. Jin is on equally bad terms with his father Kazuya as well.
StarCraft II has this inverted with the sociopathic Arcturus Mengsk and his heir apparent Valerian. Come Heart of the Swarm, he's pretty much openly abandoned the Dominion, and Arcturus is apparently content to kill his son alongside Kerrigan in order to see her dead.
In The Gamers Alliance, Seven Sisters, the eldest daughters of the higher demoness Jahi Gallu, are very much antagonistic towards their mother. Each of them represents a different sin from her youth and actually use nicknames based on those sins such as Lust etc. They've ended up working for archdemon Vaetris, Jahi's Evil Former Friend, because they believe Jahi has gone soft and cares too much for the other races. The sisters' personalities range all the way from Ax-Crazy to Manipulative Bastard to Noble Demon with Wrath being the craziest and Sloth being the most sympathetic of the bunch.
The 90's X-Men cartoon featured an adaptation of the Proteus arc, albeit one with a more positive ending: Kevin is ultimately calmed down and reconciles with his mother and father.
Season 4 Episode 4, "The Sins of the Son", featured Charles Xavier's son, David, whose resentment towards his father for his perceived abandonment of him has created two alternate personas: Ian and Lucas. Lucas, who hates Xavier, orchestrates David's apparent kidnapping as a way to lure Xavier to him; during their confrontation, Ian and David are accidentally erased, leaving the telepathic and telekinetic Lucas free to do as he pleases...exactly as he planned it.
Wolverine's Opposite-Sex Clone, X-23, behaved like this during her first appearance, targeting Wolverine for the role he played in her creation and subsequent misery. It's very much portrayed as an angry daughter attacking her father; unlike the incident with David, it has a happier resolution, with X-23 ultimately pulling a Heel-Face Turn.
On Gargoyles,Thailog, a clone, has this relationship to his "father" Goliath, and to a lesser extent his other creators, Xanatos and Dr. Sevarius. While he considers Goliath "weak," he rejects the latter two for trying to control him, but he certainly inherits their propensities for manipulation and evil.
Spider-Man: The Animated Series features an adaptation of the Carnage storyline. When Dormammu returns The Symbiote to Venom, a part of it attaches to his cellmate, Kletus Cassady (who in this adaptation is a Mad Bomber rather than a Serial Killer), creating Carnage. The two of them briefly work together as Dormammuís Co-Dragons, referring to one another as "offspring" and "dad". Following Carnage's attack on Venom's crush, however, and the latter's subsequent capture by Spider-Man, Venom undergoes a Heel-Face Turn and ultimately sacrifices himself to destroy Carnage and end Dormammuís Evil Plan.
El Tigre: Manny Rivera's Granpapi wants him to become this. Granpapi himself was this to his own father, whose father was this to his father. The Rivera family is a chain of this.