In Ai Yori Aoshi, Aoi's mother took Miyabi Kagurazaka in after her parents, who had long served the Sakurabas, died in a car accident, and considers her her other daughter. Miyabi officially gets adopted in the Distant Finale.
China raises some of the East Asian nations, but they see him more as a brother than a father. In fact, Korea refers to China as "Aniki" ("Bro"), a rather informal term for "older brother": this is pretty important since the others don't fully acknowledge China as a brother — Japan and Macau call him "Mr. China" while Taiwan and Hong Kong refer to him as "teacher".
Same with England and young America. Despite what bash-happy might tell you, they also have an older brother/younger brother relationship, with America at first calling England "Big Bro" (or at the very least offering to, but England, having less than stellar experiences with his own brothers, says "just England is fine") and later telling him that they're not brothers anymore.
Hungary and Austria were like this towards North Italy when he was a young child. Also Spain, to South Italy.
In Basilisk, male lead Gennosuke Koga is raised and trained by both his grandfather Danjou and his maternal uncle Hyouma Muroga, who was just out of his teens when he took up the role. His girlfriend Oboro, on the other hand, is raised by a nanny (who later dies) and her grandmother Ogen. Also, Oboro's fellow Iga ninja Koushirou was pretty much raised by his Evil Mentor, Tenzen.
In Battle Spirits Brave, Dan essentially adopts En and Fant, two infant mazoku who lost their parents.
Berserk: Due to Midland being a real Crapsack World and Abusive Parents and pedophiles running rampant. Guts is the sole legitimate father figure and protector of children though sometimes he can't. It's due to the horrific abuse Guts suffered as a child at the hands of his surrogate father Gambino that Guts tries to make sure no child suffers like he did.
Rickert has looked up to Guts ever since he saved him during Gut's first siege on a castle so it's natural he sees Guts as a heroic father figure/Big Brother Mentor. Rickert always defended Guts from Corkus's jibes and was deeply sad when Guts left the Hawks. Rickert was delighted at Guts's timely return but is horrified later when he discovers Guts and Casca as the only survivors of the Eclipse which Griffith caused.
After Guts tells him about the Eclipse, Rickert is not swayed by Griffith and his kingdom of Falconia, slapping him when Griffith offers him to join his new band of hawk showing Undying Loyalty to Guts.
Jill came to see Guts in this light, especially since her own father Zepek was a gambling, abusive piece of shit. After Guts saved her from bandits, covering her in his cloak like blanket (something he does with Casca later), Jill hardly wants to return to her home life and seeks Guts again. She trusts Guts so much she falls asleepon him◊ and still trusts Guts after seeing and experiencing the worst of him. Despite Jill's wish that Guts take her away from her village and horrible homelife, but Guts refused saying she would just get swallowed by his darkness and that she should be fight her own battles.
Isidro could be Guts jr and nobody would think twice, Isidro left his village in pursuit of legend of the "hundred man-killer" (who is Guts). Isidro was drawn to the swordsmen and claimed he'd follow in Guts's foot steps and become legendary. Guts, liking the boy's spirit trains him halfheartedly in very similar manner to how Gambino (Gut's adoptive Dad) trained him note though thankfully without the horrific abuse. Neither Isidro or Guts admits how much they care for each other, Guts even keeps watch of him in secret, after Isidro storms off in Enoch Village.
Schierke had seen very few other humans due to her sheltered upbringing, but comes to strongly admire Guts forming a none too subtle schoolgirl crush on him. But soon their relationship becomes father daughter-like especially after Schierke guides his soul. Like Jill, Schierke has a serious father complex when comes to Guts.
These three kids in particular Guts is very Papa Wolf over.
Blacksmith Godot despite his grumpy old man deamonor adopted Erica when her actual parents were killed in war. Godot also looked after Ricket and taught him his trade when Guts went on his Roaring Rampage of Revenge, hell he even lectured Guts like a disappointed dad when Guts came back to find Casca gone.
Daikichi of Bunny Drop acts as the father figure of Rin, a young abandoned relative he took in and raised (before eventually becomingher love interest after a ten year timeskip). He also becomes the father figure of Rin's friend named Kouki, so much so that Kouki proudly declares that he would be happy if Daikichi were his father, and when his mother does remarry, he still considers Daikichi more like his dad than his actual step-father.
In the Captain Tsubasa manga, Misugi's girlfriend Yayoi (who is stated to be a nursing student in university) temporarily becomes this to Hyuga's younger siblings when Hyuuga's mother becomes seriously sick and, due to his conflicts at work, Hyuga (who had a Promotion to Parent in the past) can't directly take care of them any longer.
A Certain Magical Index: Accelerator and Last Order are taken in by Aiho Yomikawa, an Anti-Skill officer, frequently helped by Dr. Kikyou Yoshikawa. Later in the series, Misaka Worst joins the group. All of them greatly benefit from having authority figures around that both respect them and they can respect in turn.
Code Geass: Word of God from the staff as well as C.C.'s Japanese voice actor categorize LelouchLamperouge and C.C.'s relationship as mother and son. In lead-up finale episode, she remarks to an Ex-comrade in the final battle that she doer sn't know if she loves him. Multiple times she has been shown to be there for him. She's seen comforting Lelouch in non-romantic ways like after he performed a Mercy Kill on an accidentally Geassed Euphemia. In Season 2 when the audience gets a look at Lelouch's mother who is revealed to be just as much of a Manipulative Bastard as his father you can easily see who is the more genuinely affectionate and maternal figure. Hint: C.C. and not the actual mother. In fact, 10 min into episode 21 of R.2 Marianne is peppering her words with sugary bullshit to get him to agree to hand over C.C. so that she and Charles can finalize their Assimilation Plot. But thanks to Relationship Writing Fumble, it look like something else to some fans.
In D.Gray-Man, Cross is this to Allen when he first found the boy as shown in Chapter 206, where said character admitted to having no idea how to care for a child. Word of God says that Cross sees Allen as his own child, and thinks that he's very cute.
It is unknown how Allen feels about Cross -whether he sees him as a second father, or not. He mentions thinking of Mana as the only family he had. Lavi asks him what about Cross, and Allen responds that Cross is a demon. However, after Cross is attacked by Apocryphos and believed dead, Allen shows that he did not hate his master as much as he insisted. He appears to be horrified, possibly near tears when he sees the blood in Cross' room for the first time. And he didn't take kindly to Director Lvellie casually lounging in his master's room after the incident. When he comes face to face with Apocryphos and finds out it was he who attacked Cross, Allen attacks him in rage. In recent chapter, Allen is in Nea's inner world, where he will disappear once Nea fully awakens. He meets Cross, and speaks with him for a bit in a very touching scene. After their talk, Allen smiles and says that he was happy he got to see Cross again.
There's also a bit of potential irony to the Allen + Cross + Mana triangle. Mana was openly affectionate, and seemed to love him. Cross was very gruff with Allen and seemed to keep him at a distance. But the irony comes in when it becomes a question of whether Mana's affection for Allen was genuine, or if he knew Allen was the host for his deceased brother, and only cared about him for Nea. Meanwhile, the gruff Trickster Mentor, is the one that definitely loved him. Also, Mana is revealed to be The Millennium Earl, whom Allen hates with a passion -even though his master was the one he used to call a demon. Allen has not found out the truth yet, but it won't be happy news when it comes to light.
Urokodaki serves as one for all the orphans that are under his care, including Tanjiro, Nezuko, Giyuu and Sabito. He even carved good luck charms for them in the form of warding masks and dolls. This is one reason he didn't want Tanjiro to attend the final selection fearing he would meet the same fate as the others.
Later in the series it is properly explained the relationship between Ubuyashiki Kagaya and the hunters, early on he can be seen calling the hunters children, which eventually is shown that Kagaya means that the hunters are his children since quite many of them are orphaned, he being the leader of the Demon Hunters naturally employed a lot of orphaned people with a burning desire to kill demons; the strongest hunters in particular, the Pillars, are even closer to Kagaya, showing the utmost respect towards him, two of them, Himejima and Tokitou, outright called Kagaya their second father; financially speaking Kagaya even shares his vast wealth as a mean to pay the hunters, the Pillars are even his heirs to an extent, as Kagaya gave them a good piece of land and a big house to those who are orphans and had no heritance of their own.
Jigoro Kwajma practically became Zenitsus grandfather after taking him under his wing by freeing the troubled youth from the woman pilled with debts and Zenitsu definitely sees him as such, his death was enough to make Zenitsu turn more serious than he had ever been in the series till then, fighting the cause of his death, the traitor pupil Kaigaku, without ever relying on his trance sleep mode.
Dororo: The wandering doctor Jukai found and raised Hyakkimaru, made him prosthetics to compensate for his missing body parts and trained him to be able to fight and defend himself. Hyakkimaru's parents are still alive, but his father sold him to demons and tried to kill him several times.
Dororo is forced to take up the role while travelling with Hyakkimaru, who is smart, skillfull and an absolutely horrifying in battle, but has social and language skills of a toddler. He needs some serious help while interacting with the world outside of battle. Dororo is ten and easily annoyed despite his love for Hyakkimaru.
Bear in .hack//SIGN is pretty much the Team Mom. In the real world, he grieves at his broken relationship with his own son, and in the end of the series becomes Tsukasa's real self legal guardian.
Piccolo of Dragonball Z is one to Son Gohan (they provide the image on the main page), the offspring of his one-time enemy Son Goku. However, it's not mutually agreed on — Piccolo takes Gohan under his wing by force after Goku sacrifices himself to kill Raditz so that he can train for the arrival of the Saiyans. Fortunately, Gohan toughens up and Piccolo softens down. Soon, they are truly close enough for Piccolo to be considered a father figure. Gohan would wear a costume similar to Piccolo's when fighting on Namek (until Vegeta gave him Saiyan armor), and chooses to wear a battle costume made by Piccolo—rather than Goku's gi—when facing Cell.
Originally Grandpa Gohan was this to Goku to extent Goku actaully thought he was related to old Gohan before Raditz and Master Roshi told him otherwise. Because of his adoptive Grandpa, Goku cherishes the Four Star ball and upon meeting Gohan again Goku cried for first time in the series. Whenever Goku reunited with Grandpa Gohan in Filler or games he is delighted.
Master Roshi though is often a Dirty Old Man, is still regardless a caring grandfather figure for the Dragon Ball gang and can hold them together in a crisis e.g King Piccolo saga. Roshis students in particular hold him in high regard in contrast The Crane Hermit who abuses his students.
It can be argued that Android 16 becomes a parental figure for Android 17 and 18, his love for every living thing inspires 17 and 18 (In Filler) to do the same. 16 is exhibits strong Papa Wolf behaviour to 18 when Cell wants to absorb her and he does everything in his power to stop it, likewise 18 cares greatly for 16 and refuses to leave him despite him urging her do so.
In Endride, Prince Emilio has two: he first idolized King Delzaine and referred to him as "father," until he overheard that Delzaine killed his real father, at which point he became angry and resentful. He then met Pascal, who became his second parental substitute, only for Delzaine to later exile Pascal for his disapproval of the Babylon plan. Pascal then spends the first cour using his parental substitute role to try to talk Emilio out of killing his other parental substitute and comforting him in his grief when Delzaine is killed by Ibelda instead.
Martial artist Kazuma Sohma takes his nephew Kyo in and serves as his father figure. Eventually, he also takes Rin in.
And before that, Rin was "rescued" from her Abusive Parents by Kagura and her parents. The rescue was genuine, but poor Rin was so messed up by her abusive situation that she simply couldn't accept or fit in with a more stable/happy family, and distanced herself from them.
Yuki's older brother Ayame offers to act as a literal Parental Substitute, to make up for the years when he was an Aloof Big Brother to Yuki. He seals the deal by showing up the parent-teacher conference and stopping their domineering mother from planning Yuki's whole life. And in time, Yuki realizes that Tohru, though his own age, was more of mother-figure to him than a love interest.
It's mentioned that even before their mom died, and especially after, the Rockbells' home was a home to the Elrics as well.
Izumi Curtis also seems to consider the Elrics to be surrogate sons... not that this means she's ever going to go easy on them.
There's also plenty of fanfic that promotes Roy Mustang to father figure for any of the teenage protagonists. One of the novels actually has Ed being mistaken for Roy's son, and the parallels are made pretty clear.
In the 2003 anime version, Sloth is this to Wrath. He has a living mother but loathes Izumi for "abandoning" him and they don't reconcile until much later.
In the 2003 anime Maria Ross becomes a bit of a maternal figure towards Edward. She isn't as close with Ed as he is to Izumi but they have their moments, such as the Cooldown Hug she gives him.
Chibi from Ginga: Nagareboshi Gin comes to love his foster dad Moss the mastiff after his father Kurojaki dies.
In Girls und Panzer, during the "Little Army" prequel manga, it's shown that Sakuyo, one of the Nishizumi family maids, was this to Miho, providing her advice and support.
Gintoki from Gintama acts as Kagura's dad figure sometimes. He and her real dad joined forces to freak the hell out when she got a "boyfriend."
When Shiina of Gourmet Girl Graffiti was younger, her mother had a busier job. Tsuyuko the family maidservant became her mother figure.
Although Nagi wishes he were more of a boyfriend, Hayate seems to be playing this role for her in Hayate the Combat Butler. Maria is her mother figure, though the role originally seemed to be that of big sister.
Hinagiku and Yukiji found the Katsura's to be both willing Parental Substitute and get to play the Happily Adopted card when their parents dropped a large debt on them and disappeared.
In the character profiles, Sakuya is said to have been raised by her two butlers and her nurse, instead of her parents, while also serving as the parents to her siblings.
In the Hellsing manga and OVA, Alucard acts a little like a father surrogate and mentor to Seras Victoria, who is orphan and has lived in orphanages since her parents' terrible deaths. Integra Hellsing also fills in as Team Mom on occasion (at the ending is more prominent when she literally lectures Seras as if a child) when she's not having Les Yay with her.
Hell, even the Les Yay moments made her seem motherly; feeding Seras her blood from her index finger as a mother would feed a baby from their...well, nipple. The way Integra spoke to Seras in the manga during that scene was also very motherly.
Father Alexander Anderson acts like a surrogate father and teacher to Maxwell, Heinkel, Yumie, the rest of Iscariot, and the children at his orphanage in Rome. His most human and compassionate moments involve the children he's raised, which includes the majority of Iscariot's ranks. It's the main reason why they're so loyal to him.
His final words were to remind his children to say their prayers before bed.
Highschool of the Dead: Ever since Takashi's group rescued Alice, Saya and Hirano have essentially taken on the responsibility of looking after her, as if she were their 'daughter'. Which includes bathing her, grooming her, and protecting her. Alice has grown equally attached to them, and often sleeps in the same room as Saya. By chapter 29, they've practically become a family.
Katekyō Hitman Reborn!: The aforementioned Reborn did more to raise the protagonist Sawada Tsunayoshi in one year than Tsuna's biological father Iemitsu did over the course of his entire life. Fanon frequently emphasizes this, canon lampshades it, and even the series' wiki points it out.
Played with regarding Fate's relationship with Arf. When they first meet and Fate saved her life by turning Arf into a familiar, Arf found out about mothers and wondered if Fate technically counted as her mother. While Fate does show a maternal side to Arf, their relationship seems closer to sisters then anything.
Nanoha had intended to be this for Vivio in StrikerS by acting as a temporary guardian until she could find her an appropriate foster family, though she ends up officially adopting her at the end of the season. The only reason she didn't consider adopting her right away was because she felt that her high-risk job as a military officer would make her unsuited to raise a child (not helped by the fact that she had already sustained near-fatal injuries in the past).
Lindy plays with this a bit. Unlike with Nanoha and Vivio, her plan from the beginning was to adopt Fate as her daughter; she was just giving her time to sort out her feelings regarding Precia.
In Mazinger Z, Dr. Juuzo Kabuto raised his grandsons after their parents died in a lab experiment gone wrong. After his death, Prof. Yumi took Kouji and Shiro in. However Kouji was Shiro's main parental substitute (although somewhat absent, since Kouji had to split his time between taking care of the household chores, going to school and fighting Mechanical Beasts). After the end of the series, Kouji and Sayaka left Japan for a while, and Shiro was left behind in the beginning of Great Mazinger. He was taken in by Professor Kenzo Kabuto, which is ironic, since he his -and Kouji- REAL father. In UFO Robo Grendizer, Dr. Umon found and took Duke Fleed in, treating him like his son.
The titular characters of Michiko & Hatchin develop a familial bond over the course of the anime. Hatchin's mother is unknown and presumed deceased, her father is a deadbeat who leaves her not long after they're reunited, and her foster family is abusive. Despite the fact Michiko kidnapped Hatchin from her foster parents, they're shown to have a strong love for each other even if they don't get along all the time.
Miss Kobayashi's Dragon Maid: According to Tohru, Kanna's parents were very neglectful. So when she was banished to Earth, she ended up latching onto Kobayashi as a mother figure since Kobayashi actually pays attention to her. Kobayashi later takes in Ilulu as well, after the latter performs her HeelFace Turn.
In Mobile Suit Gundam Seed Destiny, Gilbert Durandal is maybe Rey's adoptive father, but at least he is a parental figure for both Rey and Shinn. It can be interpreted as manipulation, but he appears to genuinely love them. He actually forgives Ray for shooting him, as in "forgive just before dying".
12 year old Shakti takes in a baby named Karlmann early in the show, as he was orphaned in a Zanscare attack. Shakti takes care of Karl for the rest of the series (helped now and again by the others, but she's the primary caretaker), and even in the epilogue is still shown raising the child.
The Action Girl Marbette Fingerhut is also a mother figure for Uso, Shakti, Karlmann and a bunch of children and teens hanging around the League Militaire.
Midoriya Izuku and All Might of My Hero Academia seem to have this relationship. The Midoriya family consists of Izuku and his mother, with Midoriya Hisashi, the Disappeared Dad, said to be working abroad. In Hisashi's absence, All Might meets Izuku, trains him for ten months in order to give his Quirk, One For All to him, and subsequently is not subtle in his mentorship to Izuku when he becomes a teacher at UA. In the semi-canon movie, All Might describes their relationship as thicker than blood.
In All Might's final battle, the reason that All Might is able to go beyond his limits is because All For One identifies Izuku as his successor. Izuku giving All Might the determination to live is confirmed in a later chapter.
Iruka Umino unconsciously avoided Naruto for a while because he was the living vessel for the Kyuubi, which killed his parents. After some time, though, Iruka came to realize Naruto for the person he was and realized that aside from the Kyuubi issue they were Not So Different, and by the time the series starts he acts like a Big Brother Mentor to him. Taken a step further in Konoha Hiden when Naruto asks him to come to his and Hinata's wedding as his father. Iruka accepts immediately and cries Tears of Joy when Naruto leaves.
The same goes for Jiraiya, who spent three years training Naruto and spending time with him—probably the first period in Naruto's life where there was constantly an adult around to look after him. When Jiraiya dies, Naruto is devastated. When he meets Sasuke again in the Five Kage Summit arc, Jiraiya's death (along with Pain stabbing Hinata right in front of him) helps Naruto finally understand what Sasuke went through.
Tsunade is Naruto's sole mother figure, though she didn't think much of him at first when Jiraiya brought him along to recruit her for the role of Hokage. Naruto's personality reminded her of her deceased little brother Nawaki and lover Dan, especially since they all shared the same dream of becoming Hokage. Tsunade gradually grows to care for the youth and gives Naruto Harshirama's (the first Hokage) necklace, Tsunade even goes outright Mama Bear protecting him from Orochimaru. She's is also the first woman in canon to kiss Naruto...on the forehead; even as the fifth Hokage, Tsunade does occasionally give Naruto special treatment and lets him get away with saying his opinion or acting rebellious. Naruto calls her "Granny", which is both insulting (though she is old enough) and kind of endearing. Tsuande also vouches for Naruto when A (the fourth Raikage) doubts him, betting that Naruto will be able to save the ninja world.
Actually Naruto and Tsunades bond may be even deeper if you take into consideration Mito Uzumaki is Tsunades grandmother, which means Naruto and Tsunade are indeed related.
Kakashi also counts as one. He liked Naruto from their first meeting, especially since Minato (Naruto's father) was his sensei. He even goes to check up on Naruto in his apartment to see if he's eating right, and urges him to eat more vegetables. But Kakashi opts to train Sasuke over Naruto, letting Jiraiya handle Naruto. After Sasuke's betrayal, the two did develop a closer bond, Kakashi helps him train his wind chakra and even tries to hug him when he completes the jutsu, which causes Naruto to freak out. Given that Naruto ends up becoming Kakashi's successor as Hokage and it's implied that even after that Kakashi still helps him out and advises him, it's safe to assume that their friendship/familial bond is still going strong after all those years, especially in comparison to Sasuke.
It seems likely that Might Guy and Rock Lee have a relationship along these lines.
Fanon occasionally has this as a general relationship between the teachers and students. Due to the high number of orphaned kids and kids whose family lives are either awful or unknown, it's pretty reasonable.
Gaara was originally raised by his maternal uncle Yashamaru. After Yashamaru's death, it's assumed he moved in with his father and siblings. That being said, it's implied that Rasa wasn't a very involved parent with Temari and Kankuro (Gaara, he sent assassins after), and that the siblings were mainly raised and trained by their sensei Baki, who continued to be their parental figure after their father's death.
This occurs in a Nurse Angel Ririka SOS episode about Ririka's father. He starts to feel lonely because his family is too busy to spend time with him, and is uncomfortable over the fact Ririka is becoming more independent and is developing an interest in boys. He meets a classmate of hers, who incidentally hates Ririka's guts but doesn't know that he is Ririka's dad. It's shown that Miyuki's father is always away at work and she feels left out. The two quice develop a bond. However this causes Ririka to start feeling lonely because her dad is often out "walking the dog". When she finds out about him and Miyuki she becomes jealous. Miyuki calls her out for her selfishness and states that she should be happy that she has a nice father who wants to spend time with his child.
Happens a lot in the series as most of the characters are orphaned or abandoned at a young age. The most powerful example would have to be Nami and Nojiko's foster mother Bellemere who sacrificed herself for her daughters because she refused to deny that they were hers, Nami herself struggled with the concept of Bell-mere being her mother but not sharing her blood, but at the end of the day loved Bell-mere deeply, and her death still traumatizes Nami to this day.
Genzo is seen as a father-figure to Nojiko and Nami, telling Luffy in no uncertain terms he would hunt him down and kill him if he ever did anything that took Nami's smile away. Genzo also flips out of at Nami provacative wanted posters and dress sense in true Overprotective Dad style.
Shanks towards Luffy, since Luffy's father is busy with his "job", and his grandfather was a well-intentioned yet really bad parental figure. They were so close, many thought they would be revealed as actual father and son (especially given that they even looked quite a bit alike early on, though Art Evolution has made their faces more distinct). Luffy and Ace both also had a foster mother (Curly Dadan) in their youth, again because Luffy's dad was gone and his grandpa simply couldn't fit in parental-like shoes, despite caring for them. Ace also finds this with his captain Whitebeard, since his father, whom he deeply resented anyway, is dead and his mother, Rouge, fell victim to Death by Childbirth.
Sanji originally despised his surrogate dad Zeff; completely justified since Zeff raided the ship Sanji was sailing on and beat up Sanji when he tried to defend it. However, when Sanji let slip his dream of finding the All Blue, which was Zeff's dream as well, it endeared Sanji to him so much that he dove overboard to rescue Sanji during the ensuing storm. The two were subsequently marooned on a rock for over 80 days, and survived due to Zeff eating his own leg while Sanji got the actual rations. Overwhelmed, Sanji demanded to know the reason for this kindness, and Zeff simply replied that it was because he and Sanji shared the same dream. Sanji, though he still fought with the old pirate, was deeply indebted Zeff for his sacrifice, as well as teaching him how to cook and training him to be a badass.
Sanji's loyalty to Zeff even rivals his loyalty to Luffy, and when his biological asshole father blackmails Sanji using Zeff's safety, Sanji is briefly forced to (violently) sever ties with the crew despite being the last thing he wanted. After reuniting with his crew, Sanji declared to Judge's face that he wasn't his son, at which Judge was uncharacteristically humbled.
Chopper knew no love from the moment of his birth, and doubly so after eating the Human-Human fruit and being rejected by his fellow Reindeer herd (and likely biological parents). But when he was found and saved by the questionably sane Dr Hiluluk, Chopper grew to love the quack doctor and was left in despair at his death. Despite his time spent with the superior Doctor Kureha, Chopper still refers to Hiluluk as "the greatest doctor in the world." Hiluluk also gave Chopper his name, claiming his antlers looked like they could chop down trees.
Franky loved his mentor Tom as a father, since Tom was the one who found and raised him after his actual parents abandoned him. Learning from Tom and seeing him (along with Iceberg) work so hard at building the Sea Train inspired Franky, who had been building his own battleships by that point. When Spandam of Cipher Pol used Franky's own ships to kill civilians and injure Tom, Franky had a Heroic BSoD and denounced all his ships. Tom forgives him for the injury easily, but slaps Franky when he denounces the battleships as his own, saying a parent cannot deny their child even if the child hurts people. When Tom is then arrested by The Government, Franky goes ballistic, leading to Spandam's skull getting smashed and Franky trying to stop a train with his bare hands just to get Tom back.
Robin with both Clover and Saul, maybe Zoro and the dojo owner, ... in fact, the only two members of the main crew that don't appear to have ever had a parental substitute of some sort are Usopp and Brook.
Trafalgar Law also had one: Doflamingo's younger brother Rocinante/Corazon. Who ultimately sacrificed his life to save him from Doflamingo himself.
Admiral Sengoku had a Number Two, whom he took in and raised when he was a child. Said Number Two was the aforementioned Corazon.
Word of God states Gekko Moriah found Perona when she was a child and has raised her ever since, so she views him as a father figure. When she heard of his "death" she was deeply saddened, and when she finds out he's still alive, she rushes to join back up with him.
Since Rebecca's mother died when she was young and her father isn't mentioned, the Living Toy Thunder Soldier is the closest thing to a father she has, having watched over her ever since they met. Subverted when it's revealed he is her father, who was turned into a toy by Sugar.
For a spoilery example Kin'emon isn't Momonosukes true father, but a parental substitute. Oden and Toki, Momonosuke's real parents, both boiled/burned to death. Kinemon and Momonosuke are so similar (perverted) that Straw Hats were completely duped into thinking they were father and son.
Its clear Pedro was Carrots father figure being her Mentor Archetype and very protective of her. As seen when Pedro told Luffy to turn the ship around immediately when he learns Carrot smuggled on board the Sunny which was sailing to Whole Cake Island. Carrot was a crying mess when Pedro performed a Heroic Sacrifice.
Hitetsu is this for Tama in Wano being the dual role of mentor and father figure, Hitetsu is very protective of her like when he discovered Luffy ate her rice (her first meal in years), he flipped out and attacked Luffy furiously. Hitetsu also scolds Tama frequently showing how much he cares for wellbeing. Before Hitetsu, Ace actually looked after Tama, a role that went to Luffy after Ace failed to return to Wano due to being dead.
Toko gets four Parental Substitutes: Hiyori as Toko serves as her kamuro, Hiyori takes it upon herself to look after Toko the best she can and even protects her from Shogun Orochi. Also Zoro, who lets Toko sleep on him and runs off after Toko when she tries to stop her father Yausie getting executed and saves Toko from getting shot by Orochi. Then Zoro hands Toko over to Sanji, who incidently gave Toko some of his soba noodles earlier on and cradles her in his arms while he fights off X-Drake. Then there's Robin who rescued Toko from Orochi's wrath eariler (despite being hunted herself) and after Yausie is killed and Hiyori is awol, Robin looks Toko herself and cradles her while she sleeps.
Kappa Kawamatsu took care of Hiyori after Kaido burned her parents to death, and did everything he could to bring her smile back also similar to Zeff, Kawamatsu gave all the food to Hiyori while starving himself. Fearing his safety Hiyori, left the kappa when she was 13 and fell under Kyoshiro's wing. However when reuinted with Kawamatsu, Hiyori shed Tears of Joy showing how much she missed him.
Ooku: Shogun Yoshimune's three daughters refer to Sugishita, their mother's male attendant (and later Senior Counsellor of the Royal Harem) as "father", despite him being sterile and having fathered none of them.
Yuuta Segawa from Papa no Iukoto o Kikinasai! was just a 19-years-old college freshmen when his older sister Yuri asked him to take care of her daughters Sora, Miu and Hina for a week while she and her husband Shingo were gone on vacation... then they died in the air flight. The three girls would be separated into different homes, taken by different family relatives; the girls didn't want to be separated, seeing this dire situation Yuura volunteered to become their guardian. The family agreed, but they're one step away of taking the girls away if the young and stubborn Yuuta fails to raise them properly...
Pokémon is especially bad about this, with insane amounts of one-shot characters clearly being raised by a (often same-gendered) grandparent.
Reversed with Misty, whose parents are mysteriously not in the picture and her older sisters are the ones who got the promotion instead and, despite not being bad persons, they're not good at it at all.
Gary is the only recurring character to have the "raised by a single grandparent" thing. Fleshed out a bit in a manga, where it's revealed that both Shigeru's biological parents are dead (it's not based on the anime but both characters are based off of Blue from the games).
Of the main protagonists, only May and Max have both their parents, but Brock and Cilan do have siblings.
Professor Kukui and later Professor Burnet serve as this for Ash in Sun and Moon.
Hiko Seijuro XIII can be seen as parental substitute to orphaned Kenshin, who he rescued, renamed and took under his wings in age of 8. Hiko may be too proud to admit it, but its clear he cares for his "stupid disciple" and will return from retirement to help him.
Kaoru tries to be this to Yahiko, an ex Street Urchin whom she and Kenshin rescued from being a borderline child slave to low-ranked delinquents. It doesn't always work.
Similarly, Okina was a grand-parental substitute to Misao.
In 3-gatsu no Lion, Akari Kawamoto, who is already acting as a parental figure for her two younger sisters, also serves as a surrogate mother figure for the meek, solitary Rei Kiriyama, even lecturing Rei when he does inconsiderate things like not answering the phone when he's sick for several days.
Moribito: Guardian of the Spirit: Balsa pulls double duty as guardian figure and bodyguard to Prince Chagum, after being hired to protect him. At one point in the series, she even gives a knife to him, a symbolic tradition of coming-of-age in her home country. Tanda even points out that her vow to protect him from all harm for as long as is necessary means she is, for all intents and purposes, his mother.
Panzer World Galient: When Marder invaded the capital of Arst, killed the King and kidnapped the Queen, Asbeth -their most loyal knight- rescued their son Jordy and ran away. From that day on, he became Jordy's guardian and caretaker, looking after him and teaching him how to fight.
As they were the oldest children of the Hyakuya Orphanage, Yuu, Mika and Akane became this to the younger kids. Yuu and Mika shared the role of the Team Dad, while Akane was the Team Mom, completed with Motherly Side Plait.
Guren is pretty much Yuu's dad, who does a much better job at being a parent than Yuu's biological parents. On the opposite, Krul is also considered by Mika as his adoptive mom (he practically says that she "raised" him), and she, too, does a much better job at being a parent than Mika's own parents.
In Shoulder-a-Coffin Kuro, the titular heroine and her sidekick come across a pair of very young and very naive twin girls and bring the two along on their journey. They find themselves having to run herd on the kids quite a bit, as well as teaching them about the outside world.
The Baba Yaga arc of Soul Eater revealed that Sid took in Black Star after the Star Clan was destroyed by Shibusen. However, not much has been made of this relationship in a parent-child sense, though it's evident Sid looks out for Black Star. If his methods do seem alittle odd at times. The reveal made sense, given the attitude towards Black Star taken by both the meister and his partner Nygus.
Continued in principle by Black Star taking Angela back to Shibusen. More likely to be 'big brother' than 'parent' given the age difference, but Shinigami agreed she'd be looked after, and most importantly the thought was there.
First, any children who were trapped in the game were adopted by friendly players in the City of Beginnings. We see one eventually; a young girl runs an orphanage with thirty or more kids.
Second, Kirito and Asuna find a little girl named Yui wandering the woods who takes to calling them Poppa and Momma, which they accept quite quickly. It turns out the girl is actually a therapy program designed to monitor the players' psychological states, but has been glitching because she was forbidden from interacting with the players. She became Yui so that she could be the daughter of two of the only happy players in the game.
In Tiger & Bunny, Maverick is this to Barnaby. He is also the man who killed both of his parents because they knew about his involvment with Ouroboros, manipulated his memories into believing the murderer was someone else and, later, into believing he was the one who raised him when Freeze-Frame Bonus reveals Barnaby grew up in an orphanage. And Barnaby is totally unaware of it.
Saria's relationship with Link can be viewed in various ways. She is Older Than They Look (possibly several hundred years old), has a mature personality for her physical age, and has watched over Link since infancy. Their relationship can be Like Brother and Sister, Saria being a Parental Substitute towards Link, or romantic.
13-year old Mirai and 8-year old Yuuki from Tokyo Magnitude 8.0 befriend a 30-something year old woman named Mari when they encounter each other after an earthquake. Mari spends the rest of the anime trying to help them get back home. Mari is a mother herself, though her daughter is younger than both Mirai and Yuuki.
Oboe is this for Hamel in Violinist of Hameln. It is not obvious for a long, long time, thanks to the Hamel's extreme jerkass facade and Oboe mostly keeping in the background (not without a reason), but in the end Hamel even directly states that Oboe is only being he'll ever call "father" when confronting his Big Badbiological parent.
After episode 10 of Your Lie in April, Saki's college best friend Hiroko becomes this to Kousei. She had known him from a young age and even encouraged Saki to teach her son the piano, though she later regrets it due to the emotional damage it caused him. Though, it was implied she already become this immediately after Saki's death, it was just she don't want to be near Kousei's life if her existence would bring his bad memories back.
In Yu-Gi-Oh! 5D's, Yusei, Crow and Jack were taken in by Martha when they were young. Crow himself becomes one to several children.