Berserk: The Kushan Emperor Ganishka is revealed to have killed his father (after having killed his little brother, favored by their mother). He ends up poisoned by his own son years later, and would have died had he not triggered his Behelit, transforming him into an Apostle.
Guts kills his own father (figure) Gambino at a young age, when Gambino got drunk one night and went into his tent to try to murder him. He blamed Guts for the death of his lover Sys (Guts' foster mother) from the plague. There was considerably less angst after that, especially since Gambino admitted that he was the one who sold Guts to his rapist Donovan for three silver coins.
In Madlax, Margaret Burton killed her own father Richard in very tragic circumstances. (He had been driven insane via the local Brown Note, she did it on self-defense). She blocked out the memories so well, they created a Literal Split Personality: the titular Madlax. (Or better said, two: the third one is the local Creepy Child, Laetitia).
Suzaku Kururugi from Code Geass fell into despair and killed his father, who happened to be Japan's First Minister, in order to make the Japanese troops surrender and stop the bloodbath caused with their (losing) war against Britannia.
Thanos had his mother killed to go with the many others he would eventually slaughter to please Death.
Thorgal: Thorgal is cursed by the gods for (unknowingly) killing his own father.
Emperor Commodus from Gladiator murdered his father, Emperor Marcus Aurelius, in order to become emperor himself.
Tonny from Pusher 2 kills his father in the climax of the film after having been belittled and antagonized for too long.
In one Judge Dee story, the murderer was the victim's son, who had been having an affair with one of his father's wives. The judge verbally destroys the guy (Chinese society at the time placing a very great deal of importance on ancestor worship), who ends up Driven to Suicide.
The Brothers Karamazov, in which two of the sons are accused/believe themselves guilty of their father's murder.
In "The Worst Crime In The World" Father Brown solves one of these.
According to legend, King Arthur was mortally wounded by his illegitimate son.
In the Harry Potter series, both Voldemort and Barty Crouch, Jr. killed their respective fathers.
In Warrior Cats, Brokenstar killed his father in order to become leader - as deputy, he was Raggedstar's successor.
And like his son, Raggedstar kills his own dad, a kittypet named Hal.
In Death: Immortal In Death reveals that Eve Dallas killed her own father when she was 8 years old. She had been suppressing memories of that time for years. As the series goes on, it is revealed piece by piece that her father Richard Troy raped her and abused her for years, and that he intended to make her into a prostitute and sell her to child molesters. He caught her trying to feed herself and forced himself on her to punish her. Her arm got broken, she went crazy, and she managed to grab the knife she was using on the food. She killed him with the knife. If you do not feel sympathy for her over this, then you have no soul!
In A Song of Ice and Fire Tyrion kills his father after years of psychological abuse and discovering that he had deceived him into thinking his wife and first love Tysha had been a prostitute. A kinslayer is cursed by the gods in Westerosi society, but killing one's sire is worse than killing a brother.
In the Seeker Bears book called Island Of Shadows, Nanulak the polar bear/grizzly bear hybrid uses Toklo mainly as a hitman in order to kill his polar bear father. Toklo backs off for two reasons: the first is that he was amazed to see the polar bear as Nanulak's dad, and the second was that he found out that Nanulak tricked him all along..
Ship Breaker: Nailer ends up killing his father, Richard Lopez in the climax of the book. Since Richard was a drug addicted ex-gladiator who was seeking to kill Nailer and his friend Nita at the time, it's pretty justified.
Midsomer Murders: Though it's not shown onscreen, the episode in which the psychologist's middle-school kids are the murderers, they reveal at the end that the fall that killed their father wasn't accidental in the least.
A Luthor family tradition on Smallville. Lionel Luthor killed his parents (which would include his father), and Lex killed Lionel.
Morgana, on Merlin indirectly. She doesn't actually do the deed, but she enchants the amulet that does the deed and gives it to Agravaine to use.
Regina, on Once Upon a Time. Sadly, she really did love him, which was why she killed him. She needed the heart of the one she loved most for the curse she wanted in order to fulfill her quest for vengeance.
The randomly-generated murders in WHO dunnit make this a possible result.
Religion and Mythology
According to Buddhism, intentional murder of one's father is one of the Five Grave Offenses that will get you reborn into the lowest hell, Avici.
Greek Mythology has Oedipus. He killed his father on the road outside Thebes, although some authors also make it an accident. In any case, he didn't know it was his father at the time, and had no hesitation about killing a stranger who got in his way.
One of the major elements in the cosmogony of Warhammer 40,000 is that the Primarchs, genetically engineered Super Soldier sons of the God Emperor, were stolen and later corrupted by Chaos. His favored son Horus fell the hardest, and eventually led the rebellion against him, until they faced off in a duel. Though he (Horus) died in the attempt, the Emperor was essentially turned into a barely more than a corpse, hooked up to an enormous machine that allows his body to continue living while his spirit continues to guide humanity (literally, in the case of the Navigators).
The Playbody of the Western World begins with Christopher Mahon on the run after killing his father in an argument.
Haytham Kenway and his son Connor are on the opposite factions of the Templars and Assassins side, with Haytham being Archnemesis Dad, still both of them hope that they can form a bond and set aside their difference but alas Poor Communication Kills and Haytham tries to choke his son to death with the latter stabbing him in self-defense. Both of them feel pretty bad about this in the time they have left.
Under the Lich King's influence, Arthas Menethil kills his father for the crown of Lordaeron after being turned into a Death Knight in Warcraft III. A mook even calls him out on it, demanding to know "How could you murder your own father?"
In World of Warcraft, the last quest in the Rogue legendary quest chain in Cataclysm is called "Patricide", and involves Wrathion ordering the rogue to kill his father, Deathwing.
God of War: Like in several Greek myths examples, Zeus hears a prophecy that his son Kratos would try to kill him and usurp his throne. This prompts Zeus to kill Kratos and send him to Hades, in turn prompting Kratos to escape and kill Zeus.
Shows up in the lore on the Masque of Clavicus Vile in The Elder Scrolls II Daggerfall. A disfigured noblewoman named Avalea used to masque to improve her reputation leading her to marry a powerful baron (the masque doesn't improve her looks instead making her more charming and influential). Of course, the Daedric Prince takes away his masque after a year and a day and a pregnant Avalea is banished from the baron's realm. Unusually for this trope, the child is a daughter who murders the baron when she grows up.
In Mass Effect 3, if Miranda survived the events of the previous game, she kills her father Henry in order to rescue her sister Oriana, whom he has kidnapped. Seeing as he was an abusive father who only created his daughters in order to start his own dynasty, and he used the Sanctuary facility as a trap to lure refugees into being guinea pigs for his experiments to find a way to control the Reapers, nobody misses him.
In V3 of Survival of the Fittest before he's put on the island, Liam Black killed his father by cutting the brakes of the family car and causing it to crash. He got away with it scot-free.
Averted in The Lion King: Simba thinks he (accidentally) killed his father, until it's revealed (to him) that his uncle Scar did it.
You know how Ursa from Avatar: The Last Airbender was thought to have killed Azulon to protect Zuko? Well, in ''The Search'', it's revealed that she just created the poison to do so. It was actually Ozai who killed his own father to get the throne.
Timber Wolf in Legion of Super Heroes brutally murders his father in front of a live audience, however it turned out to be a clone and his real father concocted this elaborate scheme to get his son to work with him again involving nanites implanted in his son's brain. It was ultimately averted at the end where Timber Wolf refuses to kill his father.
According to Herodotus, the Persians believed that no man since the beginning of time had ever killed his own father, and that whenever this appeared to happen, it was evidence that the patricidal child was actually an impostor or changeling.