In 7 Seeds, Semimaru was raised by his night-worker mother and never had a father around and was never told who his father even was.
Most of the characters in Air either have some sort of issue with their mother, is a mother or is playing the part of one, but only one father is shown. Subverted later on, when Misuzu's father returns for her... way too late.
Grisha Yeager has been missing ever since shortly after the Fall of Wall Maria. This causes Eren quite a bit of frustration, especially since his father seemed to have something to do with his mysterious powers. Eventually, it turns out that Grisha has been dead all along. The cost of giving Eren his powers was being eaten by him. Eren does not take this revelation well.
Historia Reiss grew up without ever meeting her father, a nobleman that had an affair with a servant. He never bothered to meet her, until his other children were killed and he needed to ensure an heir still existed, just in case. When he decides she's needed, he pretends to be a loving father in order to manipulate her. He's actually the true ruler within the Walls, and after his death at her hands, Historia claims the throne for herself.
Reiner Braun turns out to have been raised by a single mother, who explained that his father couldn't be with them because the relationship was against the law. His father is a Marleyan, driving him to become a Warrior in order to reunite his parents and meet his father.
Serpico in Berserk spent his life hearing from his mother that his father was a nobleman who'd seduced her when she worked as his maid. After a while, he stopped believing it. Then he became Farnese's servant, and one day her father asked about his mother. When Serpico described her, the man murmured something along the lines of "Oh, her"... and Serpico immediately caught on. Both agreed it was best for Farnese not to know about her older brother...
Guts himself counts, since we know what happened to all of his parental figures except for his biological father. This just brings up a slew of fan speculation of just who - or what - Guts' real dad is, especially since he has many physical attributes that suggest to some fans that he might not be entirely human. Other than that, this trope is played straight with Guts' adoptive father Gambino, since he talks more about the loss of Gambino than of the loss of his adoptive mother (justifiably, since she died when he was an infant and he appears to have no memory of her).
Marika lives alone with her mother. Her father is never mentioned.
Ryousuke's parents are separated. When his mom is sent to a mental health hospital for therapy he is sent to temporarily live with his dad.
In Captain Tsubasa, Tsubasa's father works abroad (though he makes efforts to keep contact through letters and visits) so Tsubasa is raised mostly by his mother and later by both her and Roberto Hongo, Dad's best friend. Additionally, Kojiro Hyuuga lost his father at an early age (in an accident, the manga says; of illness, the old anime says, though to be fair the issue came up years later) and runs part-time works to help the mother and siblings he adores.
In Cardcaptor Sakura, Tomoyo's father doesn't seem to exist, and Sakura muses to herself that it seems to be a "complicated matter", but thinks that he most likely is still alive. Also, Syaoran's father passed away when he was very young.
With Tomoyo, it's at least hinted at the manga that Tomoyo's mother Sonomi may be a lesbian like her daughter... and likewise with a crush on a cousin (Sakura's mother). If that's the case, it's not surprising that the marriage would involve separate households. There are quite a few theories on how Tomoyo was born.
The kids' relationships with their families tend to be important in Digimon. Sora's dad Haruhiko is never referenced in the first season, and her ultra-traditional mother Toshiko is emotionally distant (although she gets an awesome moment of Mama Bear when pushed). A lot of Sora's character development plays into mending their relationship, but Dad isn't mentioned until halfway through the second season: he's a famous researcher who spends a lot of time away from home. (Ironically, according to the drama trackA Letter To My Father, in his wife's hometown.)
Jou's dad is The Ghost until the CD dramaMichi e no Armor Shinka. He's emotionally distant, wants his three sons to all be doctors like him, and this causes some friction. The anime gave very little resolution to this, having Jou's decision to be a doctor seem rather sudden, but Armor Shinka and another drama track, Telephone, show that Jou decided to become a doctor because the Digital World didn't have any of its own and that his father did eventually rethink his positions and told Jou that it was okay if he made his own choices. So basically, Jou did become a doctor, but it was the way he wanted and not because of Dad forcing him anymore.
In Digimon Tamers, Juri's father isn't a bad person per se, but is very emotionally distant for reasons described under Missing Mom, and Ruki's father is nonexistent. Her mother, Rumiko, is a supermodel who had her at a very young age and they both use the father's surname, but whether he's missing because of divorce or death is contested. In the English dub, at least, Rika compares her situation to Jeri's, saying that she doesn't see her father very often, but at least she can and implies that's mostly her own choice, but the movie Runaway Digimon Express shows her to remember him fondly and might imply he's dead. Of course, that movie is also Canon Discontinuity.
In Digimon Savers, Masaru's father Suguru is notably absent. It turns out that he was left behind on the first expedition to the Digital World and, after being imprisoned and supposedly executed by Yggdrasil, ends up sharing a body with Banchouleomon
You could argue this for most of the dads in the Dragon Ball Z canon. Goku's father Bardock and adoptive grandfather Gohan are both dead before the series begins and seems to be this a fair amount himself what with spending one year dead, a year training in space, dead for seven more years, and abandoning his family ten years after that to train the reincarnation of the last Big Bad. Vegeta's father, King Vegeta, was also killed off when he was a child; in the alternate timeline has himself been killed so that version of his son grew up without a father. In the main timeline, he's shown to be present but extremely distant on both an emotional and psychological level with his son, at least until his Final First Hug. His relationship with his daughter Bra is more difficult to evaluate due to matters of Fanon and Fanon Discontinuity.
Dragonball Abridged plays up Gohan's developing anger issues with his increasingly absent and ineffective father.
Shobu's father from Duel Masters seems to have disappeared into thin air before the series started, which is given a Lampshade Hanging or two in the dub.
Renton suffers from this in Eureka Seven, and is eager to find out what really happened to his dad (ep. 38).
In Fruits Basket, both Tohru Honda and Akito Sohma's fathers died when they were very young. Both of said deaths marked the start of a rather unpleasant stretch of time in both of their lives though Tohru's mother Kyoko did get her act together eventually. Kyo's father is still around but refuses to interact with him at all, so he was raised by his martial arts instructor. Pretty much every other Zodiac character doesn't have a father seen onscreen, though a few are mentioned in passing: Uotani's father was a drunk who ignored his daughter after his wife left him, but it was implied that after she got her life together, she started making him fix himself up.
In the manga, Uotani's bad home life with her father is shown, as is her getting him sorted out once she is.
Fullmetal Alchemist: Hohenheim left the family when Ed and Al were very young. He did have huge reasons, namely preventing his evil blood-related creation from absorbing the entire country into intself, becoming god, and conquering the world, but Ed is (understandably) still bitter about it.
In the 2003 anime, Envy is a bit more bitter about it than Ed is, which leads to his extreme daddy issues and eventual patricide.
Hayato's father in Future GPX Cyber Formula, who is the creator of the supercomputer system Asurada. Hayato wanted his father to see him in his races... until it's been revealed by his mother that his father was dead all along.
In Gakuen Babysitters, both of the Kamitani siblings are estranged from their father ever since their parents divorced. Though emotionally distant, they are still physically close, since their father is one of the teachers in the school.
Guyver has one of the most brutal subversions ever. Sho's father was turned into a Guyver-killing Zoanoid who damaged Guyver 1's brain. The Guyver, on autopilot, killed Mr. Fukamachi, but Sho didn't remember it. He eventually found out and developed a psychosomatic block against activating the Guyver, until Aptom threatened Mizuki and forced him to change. What's even more painful is that while this all happened in the manga (and the most recent anime repeats it all, sometimes panel for panel), the anime specifically spent much more time on strengthening Sho's relationship to his father.
Haiyore! Nyarko-san: According to Mahiro's mother Yoriko, his father is stuck working overtime to make up for the time they took of for their eighteenthhoneymoon. Unfortunately for poor Mr. Yasaka, he was stuck in this off-screen limbo for the entire novel series, never appearing even once.
Hanaukyō Maid Tai. Taro's father does not appear in either series. It was mentioned at the beginning of the first series that he was a painter with whom Taro's mother eloped.
In Hunter × Hunter Gon's primary goal in becoming a hunter is finding his vagabond father Ging.
Kagome's lack of father has sprouted some Epileptic Trees (He's really a demon, he's really Sesshomaru, he's really InuYasha, etc.) The truth? The NovelizationShutetsu Inuyasha reveals that Papa Higurashi is actually dead as a doornail, and that happened in a car crash when Kagome was a little girl. This is the reason why she and her family live in the Shinto shrine with his father, too.
JoJo's Bizarre Adventure runs on this trope. If you're a main character in this series, it's guaranteed that you're going to barely know your father, if at all. Part 1's Jonathan Joestar's father is killed by Jonathan's adoptive brother Dio Brando; Part 2's Joseph Joestar didn't even know his father, since he died before he was born; Part 3's Jotaro Kujo's father is a career musician who is frequently away on tour; Part 4's Josuke Higashikata was conceived during a one-night stand between an elderly Joseph and a young woman he met; Part 5's Giorno Giovanna's father, Dio Brando, was killed by Jotaro during the events of Part 3; Part 6's Jolyne Kujo suffers from the same daddy issues that her father Jotaro did in his youth, although in this case it's slightly subverted as Jotaro distanced himself from his daughter for her own good; and Part 7's Johnny Joestar's father actually DOES happen to be present in his life, but he resents Johnny due to him accidentally killing his older brother.Whew.
The video games All-Star Battle and Eyes of Heaven attempt to subvert this. In ASB, you can pit Giorno against Dio, who has a So Proud of You reaction, and in Eyes of Heaven, he beams at his son during a combo attack. You can also team up Joseph and Josuke, and while Josuke's a bit less receptive, he eventually warms up to it. As for Jotaro and Jolyne? Jotaro takes advantage of a brand-new timeline to attempt to be a better father to her. Awww!
Kamisama Kiss begins with Nanami Momozono's dad walking out of the house and her life without giving her any real warning...and leaving her to face his angry creditors.
Many jokes have been made about the non-existent father of Kanon's Nayuki. Could he have been the secret ingredient of Akiko's jam? Also, Mai has a plot-important mother, but her father isn't seen anywhere.
Iemetsu Sawada of Katekyo Hitman Reborn! pretty much fits this trope; he had been away from home for over two years, according to Tsuna, who once expressed the thought that he was actually dead.
He does do his part in the family, however, and seems to send an undisclosed amount of money to his cute wife, Nana—as she confirms this—and doesn't seem to have any kind of job. But Iemetsu is blatantly irresponsible, and has been caught getting the toddlers drunk, and to top it all off, he's pretty much second in command of the Vongola.
Kore Wa Koi No Hanashi, Haruka's father is very rarely at home, or even in the country, due to his work. He eventually gives Shinichi guardianship over Haruka, after realizing how much time she's spent at his place.
In Gourmet Girl Graffiti, we have seen Kirin's dad on-screen and living with Kirin. Ryou's is offscreen, but at least he has been referred to. Shiina's dad, however, was never mentioned at all.
The tititular character of Kubera is shown to have a missing dad in the very first chapter. Later we find out his disappearance is even more mysterious and that he's presumed dead, even though he was spotted on the last spaceship coming back from a destroyed planet. He was never seen after the landing, but on the ship he was seen uncharacteristically crying about not being able to see his wife and unborn child.
Ayumu and her sister from Life only seem to live with their mother.
In Love So Life, Aoi and Akane's father abandons them following the death of their mother, leaving them in his brother's care.
The weirdest example I can think of is in Loveless. Ritsuka's dad is still in the vicinity, but you'd be forgiven for thinking otherwise. We seldom see him, and after Seimei's departure he doesn't do much to protect his son from his mentally unhinged mother Misaki. This is dismissed by Ritsuka as "he's working all the time," but he basically leaves his child in mortal danger. Mind you, very few people in the Loveless universe seem to give a damn about child abuse.
Miyuki from Lucky Star is shown to only live with her mother. Though on the Valentines Day episode (or clip..whatever..) she said she would be giving chocolate to her father. So he's either out traveling or divorced. (Though, Miyuki's mother Yukari never talks about him either).
There is no mention about Minami's father either, although Minami's mother, Honoka, is.
The closest thing to a parent figure in the Yagami household would be Hayate. There's Hayate's mysterious "uncle" who supported her financially when she was young, but was actually planning to seal her along with the Book of Darkness.
We only find out what happened to Chrono's dad Clyde when the artifact that killed him becomes a plot point. His widow Lindy also adopts Fate, Erio and Caro, extending the Disappeared Dad trope to them.
Speaking of Fate, where's Precia's husband anyway? We don't even see a father in the flashbacks to before she lost her mind.
Vivio's situation would get conservatives' knickers in a twist since she Has Two Mommies. In this case, it's less of a 'Disappeared Dad', and more of a 'Dad? What Dad?'. Yuuno/Nanoha shippers, however, find evidence that he acts as a third parent; Fate/Nanoha shippers are just glad for the two.
Vivio suggests in the "Second Mother's Day" one shot that Fate is like her father, and gives her a gift for Father's Day.
Lutecia's plot revolves around her trying to make her comatose mom Megane wake up again. As for her dad... well, we don't even know what he looks like or if he even exists since he's never mentioned. She does temporarily get a father figure in Zest though.
If all THAT isn't enough, in Triangle Heart 3: Sweet Songs Forever, we have Fiasse (dad murdered by terrorists), Shinobu (pretty much abandoned with her maid), Miyuki (dad murdered by terrorists, adopted by relatives, new dad also murdered by terrorists)... yup, that means Nanoha's dad Shirou, one of the few in Nanoha, is dead here too. And he actually died when Nanoha was still in Momoko's womb, to twist the knife even further.
Negi Springfield's ultimate goal in Mahou Sensei Negima! is to follow in the footsteps of his legendary father Nagi, known as the Thousand Master. Nagi disappeared ten years prior to the series start and was assumed dead, but various characters and events have stated that he is very much alive, although his whereabouts are still unknown. Negi also has a Missing Mom, but for some reason he didn't seem even remotely interested finding her. Until recently.
Maid-Sama!: The female protagonist's Freudian Excuse to hate men was her father abandoning her, her sister and her mother and leaving them in debt.
Kouji and Shiro (The Hero and his Annoying Younger Sibling). They were missing their father, Kenzo Kabuto, after he died in a lab experiment gone wrong. Years later they found out he was not dead. And shortly after they found about it, got used to the idea and got over their abandonment issues he died in Great Mazinger. For real this time.
Sayaka Yumi -Action Girl and female lead- belongs to the "her father is physically present but he is barely there" category. Her father was Married to the Job, and getting the responsibility of saving the world dumped on his lap has not improved the situation. At least he tries to take care of Sayaka, but she knows his family is secondary to his job in the Institute, and she feels neglected.
Yuri, Sayaka's cousin. The main reason of she developed a demanding-attention, cranky attitude was her parents were always away, leaving her alone constantly.
Hiroshi, son of Dr. Kasuya, a scientist worked in the Institute. His father disappeared in a car crash, but the body was not found. He refused to accept his father was dead. How it turned out, he was right.
The series revolves around a woman, Michiko, kidnapping a presumed orphan, Hatchin, to lead her to her father who the woman is in love with. Hatchin has never met her dad and doesn't show much interest in him. In the final episode Michiko sends Hatchin to live with her father. This ultimately bombs when Hiroshi ends up ditching his daughter for a woman not long after.
In the Distant FinaleHatchin has an infant son and it's mentioned his dad left after three months.
Kira Yamato had two parents in Mobile Suit Gundam SEED. Yet at the beginning of Mobile Suit Gundam SEED Destiny, he's shown living with his mom Caridad ( actually his aunt). Dad's disappearance is never explained, nor is he even mentioned. His (and Cagalli's) actual father is Mad Scientist Ulen Hibiki, who is dead by the moment the series starts.
Cagalli's adoptive father is the King of Orb, Uzumi, and they're somewhat distanced in the beginning. He later pulls an Heroic Sacrifice to save Orb, playing the trope straight.
Flay's father George was a higher-up in the colonies, and Flay mentions that she cares very much for him but he's always working and away from her. He was then killed off in front of her, and she was so fucked up by the loss that she went from a mere Rich Bitch to a Yandere while seeking for revenge.
The father of Kira's girlfriend Lacus Clyne, Siegel, is the chairman of ZAFT. He's later killed by Patrick Zala's group.
As if saving the world wasn't enough in Monsuno, Chase Suno's father mysterious disappearance becomes a plot point for most of season one, as he and his friends try to find him.
In My Hero Academia, Izuku Midoriya's father is eventually revealed to be working overseas in order to support his family; this is lampshaded by the fact that his name is Hisashi, derived from the Japanese phrase "hisashiburi", which roughly translates as "Long time no see".
It's extremely common in the Naruto world for characters to have one or both parents missing/dead, due to the five major nations being more or less constantly at war with eachother. Sakura is the only main character whose father isn't dead, and only a handful of characters make it through the series with surviving fathers and/or father figures.
Hatake Sakumo fits this trope. After failing a mission he was basically shunned by everyone he knew, which left him depressed and eventually resulted in him committing suicide. Unfortunately this also meant abandoning his seven year old son, Kakashi, whose mother had died several years before Sakumo, thus leaving him alone and without a family in a really harsh, war torn world. This is without mentioning that Kakashi most likely witnessed it.
In the the spinoff, Naruto Gaiden, it turns out Sasuke is one for Sarada since he had to leave for a very important secret mission when she was a little kid.
The whole awful mess started when Shinji's Disappeared Dad came back.
Asuka's dad 'disappeared' from her life after her mother got her mind sandblasted into insanity by Unit 02. While Kyoko was hospitalized he had an affair with the head nurse in charge of Asuka's mother. And Asuka knew about it, and they knew she knew. Didn't stop them, though. After Kyoko's death he stopped to take care of his daughter, and Asuka never acknowledges anyone as her true parents.
Misato has one too- she hated him until the day he saved her life in the Second Impact. Dying doing such a thing is what spurs her on to fight the angels in adulthood. It's also implied that her problems with her lover Kaji are at least partially caused by her daddy issues.
Luffy didn't even know he had a father, Dragon the Revolutionary, until informed by his grandfather. In typical Shounen fashion, he takes this in stride while his older brother Ace is revealed to be much more bitter about his own father, not because of abandonment, but because of how many people spoke badly of said father, which had a negative impact on Ace's self-esteem. Ace says his only father is his captain, Whitebeard. And with good reason... his Disappeared Dad is none other than Gold Roger.
This is part of Usopp's backstory. His father Yasopp left to join Shanks' crew while his wife was dying. After 10 years, Yasopp never returned and Usopp spend those years waking the entire village with the claim pirates were coming.
In Robin's backstory, we meet her mother Olvia, but we never meet her father. It's implied he's dead.
This also happened with Franky, when his subordinate Zambei revealed he's now a wanted man, he mentions his father was a pirate.
In the Dressrosa arc, we have a variation: the gladiator Rebecca's backstory does not explicitly show her father as a part of her life. Later on, after Doflamingo forcibly took over Dressrosa, her mother Scarlett would be killed despite protection from the Toy Soldier, and Rebecca would be raised by him as a Parental Substitute. This is because she completely forgot her father's existence. Scarlett was one of the two daughters of King Riku Doldo lll, the king Doflamingo deposed, and for that she and Rebecca were hunted down. Her husband, the legendary gladiator Kyros, however, was turned into a toy, and everyone forgot his existence thanks to Sugar's devil fruit powers. This toy would later on be revealed to be the Toy Soldier. So from Rebecca's perspective, her father completely disappeared from her life, while from the perspective of everyone who knows the truth (including the audience) her father raised her without telling her who he was.
Ash's father in Pokémon is only mentioned in the second episode, which only implied that he had gone on a Pokémon journey like his son at some point. This has sprouted some Epileptic Trees. (He's really Team Rocket's boss, he's the first one to actually train a Pokémon, he's Professor Oak, etc.) In a flashback, a young Ash was seen with an adult male thought to be his father, but that's as far as it goes.
According to the (Japan-only) novelizations by Takeshi Shudo (the director for the original series from Kanto-Johto), Ash's father (who the narrative doesn't name) was a random trainer who married Delia, then left and was never seen again.
This affects Dawn as well in the Diamond and Pearl season. It's even more troublesome as it seems that Dawn's father never existed at all, considering the information we are shown of her mother always traveling in contests. Then again, she's somewhat of a girl version of pre-Johto Ash with elements of Broken Bird and Stepford Smiler added.
In fact, the majority of the main characters in Pokémon have a Disappeared Dad. The only exceptions are the two pairs of siblings, May and Max in Advanced, and Clemont and Bonnie in XY (and the latter pair makes up for this by having a Missing Mom), Brock, whose father was missing but returned to his family in Brock's debut episode, and James.
In Pretty Cure, Miki lives alone with her mother, and her brother lives with the never seen father. Yayoi is a sad example as her father died when she was young. Yuri and Ako are tragic examples, especially the former. Their fathers Professor Tsukikage alias Sabaaku and Mephisto were brainwashed by the two Big Bads Dune and Noise, respectively, and became the leaders of the villains. Professor Tsukikage was absent before, because he researched the Great Heart Tree, but he never came back because he became Sabaaku. Mephisto declared himself as the enemy of his own kingdom Major Land and left it and his family, and he created the new kingdom Minor Land. However, unlike Yuri, Ako knew what happened to her father Mephisto and she knew where he was, but she's afraid that she had to fight her father. Yuri finds out what happened with her father during her final battle against Dark Precure when he protects her with his body and lose the mask that controls him. (It is also revealed that Sabaaku created Dark Precure and that she's Yuri's biological younger sister.) Like Sabaaku, Mephisto gets de-brainwashed, too, after Ako fought him. However, While Mephisto comes back to Major Land, Professor Tsukikage sacrifices himself when he protects Yuri and Tsubomi, becoming a Disappeared Dad forever.
The death of Ryo's father in Princess Nine plays a huge role in the series.
In Sailor Moon, Ami's parents are divorced and she lives with her mother Saeko; her father is a painter, and apparently spends time traveling through the world. In the anime it borders on Parental Abandonment: in one episode, Ami is going to go to school overseas and the Senshi meet her at the airport, and she eventually decides to stay. Would she really not be seen off by her mother?
In the live-action version, Pretty Guardian Sailor Moon, Usagi still has both parents, but her father is a reporter who is only ever seen on the family TV set, effectively giving her a one-parent family.
Rei's father is alive, but is also a politician who is Married to the Job and only really bothers to be a father on her birthday. He couldn't even take the time from his work to be with his wife when she was dying, which is why Rei is perfectly happy to be living with her grandfather instead.
Ann's father, who divorced Ann's mother because of his debts. She took Ann with her to Shimane and neither parents ever visited each other. Ann next sees him a few years later when he visits her to take Ann with him to Tokyo (since the mother had died earlier).
Fuji's and Shiika's mother had an affair a number of years ago, and the rumors go that the man is Fuji's biological father. He's shown to be a sleaze bag and wants nothing to do with Fuji, leaving him sickened that he is related to such a man. It is only later revealed that he's Shiika's biological father and not Fuji's.
Several School Rumble characters (The Tsukamoto sisters, Masatsugu & Haruna Tougo, Eri Sawachika, Mai Otsuka) have absentee fathers.
Word of God states that none of the characters have parents because they're not important to the story.
Science Ninja Team Gatchaman: Ken Washio's Dad was another case of Disappeared Dad who was actually right there all along as the leader of Red Impulse. And then he makes an Heroic Sacrifice and Ken is left dad-less again..
Natsumi and Fuyuki's father in Sgt. Frog. It is never really explained what has happened to him, and he only appears in the anime in a brief cameo in the seventh season finale.
In Shugo Chara!, Ikuto and Utau's father, a prominent violinist, disappeared after he was going to be forced to give up playing the violin and running the Easter company. He does return in Shugo Chara Encore though his children didn't see him.
In Tengen Toppa Gurren Lagann, the basis for Kamina wanting to leave his hometown so badly is because his disappeared dad left for the surface years ago. His father is dead; his skeleton is found by the group in the second episode (which causes Kamina a brief Heroic B.S.O.D.).
Arata Kirishima from Tokyo Ghoul. After promising that he would never leave his children alone, he was discovered by Investigators and either captured or killed by them. Touka seems to have taken the loss much better than her younger brother, Ayato, who has some very serious Daddy Issues as a direct result. The anime makes it even more painful, with Ayato battling Shinohara — the man field testing Instant Armor made from Arata's kagune. Ayato immediately recognizes the armor for what it is, while Shinohara notes that the equipment intended to enhance his physical abilities is instead making him sluggish for some reason.
Yoshimura turns out to be one. It's complicated. Father and daughter know exactly where each other are, but Yoshimura intentionally keeps his distance and denies his child's existence to protect her. Otherwise, the organization he once served will find and kill her.
Bu-ling's father in Tokyo Mew Mew is off training in the mountains, leaving her to raise her five younger siblings alone — kind of... cruel, considering she is eight years old and her mother is dead. Also, in a flashback, Kisshu's family is seen — him and probably a mother and a sister, but no dad.
Ryuuji and Taiga in Toradora!. Ryuuji's dad is dead ( Although it is later revealed he just abandoned Ryuuji and his mother before Yasuko gave birth.) He was a yakuza, and is where Ryuuji gets his dangerous looks from. Taiga is estranged from her father, since he's treated her like crap her whole life: Mr. Aisaka pretty much just sends her money and shows up once in a while to screw with her feelings, which is one of the sources of her temper. At the end, though Taiga leaves to again live with her mother and step-father, feeling she has to fix her own broken family before she deserves to start one with Ryuuji.
Initially played for laughs with Teen Genius Susumu's father on Wandaba Style. The girls went back in time and thought that he died in the ill-fated mission to the moon, but it turns out he's alive and well...in Canada. Later in the series, though, he decides to check in on his son, but does so without letting his son know he's back in Japan, mentally asking Ichirin to watch over his boy.
Saori from Wandering Son is the only one of the main four characters not to have her father shown, even with all the scenes she's at home or with her mom.
Keima Katsuragi's father, in The World God Only Knows, is implied to spend his time abroad collecting data. His absence helps newbie demon Elsee pass herself off as his illegitimate daughter. That said, he at least remembers his wife's birthday.
Subverted humorously in Yotsuba&!. When Asagi says "Dad isn't here any more", melodrama included, in the second volume of the manga, the reader's left to assume he's gone for good, but it turns out he's just at work, and Asagi is being facetious.
In Your Name, Mitsuha's father Toshiki is estranged from the family, having walked out on his daughters and left them to their maternal grandmother after the death of his wife to illness and his subsequent dereliction of his priestly duties. His section of the side novel Another Side: Earthbound goes into more detail and makes it much less one-sided than how the film proper portrays it.
Ryou Bakura's is mentioned in-story to be traveling all over the place and had given Bakura the Millennium Ring as a souvenir from Egypt but he never makes a proper appearance, and we never see Yugi's, Tea/Anzu's, Tristan/Honda's, Duke/Otori's, or any other father aside from Joey/Jonouchi and Serenity/Shizuka's drunk of a father, the dead biological parents of Seto and Mokuba, and Seto and Mokuba's adopted father Gozoboro Kaiba (manga says Seto killed Gozoboro, anime filler arc claims he disappeared into and orchestrated a virtual reality so he could take his revenge upon Seto later. And that he had a biological son who for some reason looks like a green-haired Seto.). Grandpa Moto is Yugi's grandfather and pretty much raises most of the kids when they have any parental supervision at all. Seto ends up becoming Mokuba's substitute father.
Yu-Gi-Oh! 5D's: Yusei's father seems to have bought it during the Zero Reverse incident that split New Domino from the Satellite.
Yu Gi Oh Zexal: Yuma's father was lost in Astral World several years prior to the series.
Yu-Gi-Oh! ARC-V: Yuya's father no-showed a dueling event he was scheduled to compete in and disappeared without a trace three years ago.
Interestingly for a shonen, where fathers tend to at least have a prominent role in the backstory, none of the male leads of YuYu Hakusho have plot-significant fathers. Yusuke's mother Atsuko was 14 and unmarried when he was born, and his father only appears briefly in the last volume of the manga and is unnamed. Apparently fans were so unused to this that to this day, people can still be found who insist that Noble Demon Raizen was his father instead of a distant ancestor. Kurama was born to a married couple, but his father died before the beginning of the series and his mother serves as his Morality Pet. Hiei's father is completely unknown, though the fact that he was a male born to an Always Female race implies he had one. Neither of Kuwabara's parents are important, but his father appears towards the end of the manga.