The Turn of the Screw: To the Nth degree. Miles and Flora are orphaned, and their uncle ships them off to his isolated country estate and wants nothing to do with them. They're raised by servants, especially the valet Peter Quint and the governess Miss Jessell — who then died. Did the children still have the company of Quint and Jessell after death? were the servants bad influences on them? Who knows. Certainly the new governess proved to not be a satisfactory mother figure.
Alanna: Mother dead, father emotionally distant - we see him on the first page and never again throughout the series - and later dead.
Daine: Daine is illegitimate, and by the time the story starts, her mother is dead. Her father turns out to be the hunt-god Weiryn.
Beka: Mother dead, father never even named, although we know Beka's gift is from him and his mother is a minor character. Also the numerous children who were sold by their parents as slaves, throughout all the books. In Mastiff, Beka even mentions that she'll have plenty of people in the Lower City angry at her now that they can no longer sell their children.
Averted with Keladry and Aly. Kel's parents are both alive and very supportive, and communicate by letter while she's training for her shield. Aly's parents are Alanna and George, who are both extremely difficult to kill.
Taran of Lloyd Alexander's Chronicles of Prydain was raised on a farm by two old guys, neither of whom are in any way relatives. In Taran Wanderer he tries to find out who his parents were, and ends up losing interest. Princess Eilonwy's royal parents are dead, as is their kingdom. She has an evil aunt, however. Gurgi, meanwhile, was such an orphan that nobody was even sure what species he was.
Achren was not really Eilonwy's aunt. In the fourth book, Taran Wanderer, Taran doesn't find out what happened to his own parents but does find out about Eilonwy's mother — it was revealed that Achren kidnapped Eilonwy as a baby, and Princess Angharad died trying to get her back. Additionally, the book The Foundling and Other Tales of Prydain reveals the identity of Eilonwy's father.
Ayla, the heroine from Jean M Auel's Earth's Children series, was orphaned at the age of five when her parents died in an earthquake. She seems surprisingly free of parental abandonment issues until the third book, when she begins to wonder what tribe her parents belonged to and if she has any relatives still alive.
Probably helped that she had loving foster parents (Creb and Iza) raising her.
Enid Blyton's characters have absurdly neglectful parents by modern standards, in particular the Famous Five who are supervised largely by their Uncle and Aunt... who allow them to spend most of their time unsupervised on a distant island.
Standard practice for Edgar Rice Burroughs's Green Martians. The women do not know whether their eggs were selected for hatching, and couldn't identify the fathers. John Carter of Mars attributes much of their harshness to this; one Green Martian raised by her mother, and knowing her father, is far more generous and gentle than her fellows.
Malcolm Dresden's death is way beyond being suspicious. In the TV series, it's revealed that he was murdered by Justin Morningway, Harry's maternal uncle, by means of a voodoo doll. Justin cursed Malcolm (who was in Florida) with a fatal heart attack so that Justin could gain custody and control of eleven-year-old Harry, who had come into his power very young. In Fool Moon, a demon tells Harry that both of his parents died unnatural deaths, which surprises Harry, who had thought that his father had died of an aneurysm when he, Harry, was six.
As for Margaret Dresden... in Blood Rites, Harry's mother is later revealed to have died due to a curse by her former consort and White Court vampire Lord Raith. As she is dying, Margaret curses Lord Raith so he cannot feed, condemning him to a slow death by starvation.
In Death Masks, Ivy comments that her mother went into a coma after giving birth to her. In Small Favor, Luccio reveals that Ivy's seventeen-year-old mother killed herself after her grandmother was killed in a freak car accident, passing the Archive down to her. Angry at her mother for dying and angry that the unborn Ivy would get to live the life that she never would, she killed herself once Ivy was born. What's worse is that because of the nature of the Archive (which is not only all knowledge ever written by mankind, but also the experiences of all the previous Archives), Ivy knows exactly how her mother felt about her.
In Codex Alera, Jim Butcher's other series, the protagonist Tavi is an orphan raised by his aunt Isana and uncle Bernard. Tavi assumes that he was illegitimate and that his father was a soldier killed in a famous battle around the time he was born. In fact, Isana herself is his mother and was married, but she kept it a secret that Tavi was her son because Tavi's father was the prince and heir to the throne and had been assassinated.
Kitai, the Marat ambassador, also has abandonment issues, but for more normal reasons: her mother died when she was young.
In Enders Game by Orson Scott Card, the parents of the geniuses Peter, Valentine and Andrew seem oblivious to the extracurricular activities of the elder two, as they use internet anonymity to gain influence on world affairs as political pundits. Peter in particular feels nothing but contempt for them and their ignorance. In one of the sequels to Ender's Shadow, however, this is completely inverted when the parents reveal they knew all along — but pretended not to so that their kids wouldn't be afraid to write what they needed to say. They none-too-gently chide Peter that he should have known his and his siblings' super-intelligence had to come from somewhere.
Roald Dahl likes this trope. The Big Friendly Giant stars an orphan named Sophie, Danny the Champion of the World has no mother (although she is discussed extensively), James of James and the Giant Peach is sent to live with his abusive aunts after his parents are eaten by a rhinoceros, and the anonymous protagonist of The Witches lives with his grandmother, because his parents were killed in a car accident. Matilda has parents, but they pay as little attention to her as possible; in the end she abandons them.
The royal children of Pamela Dean's Secret Country all have Missing Moms and distant fathers — which proves most convenient. As does the fact that their real world alter-egos' parents are all in Australia.
They even bring this up; "there seems to be a shortage of mothers around here" or words to that effect.
Jeremy Griswold's book Audacious Kids: Coming of Age in America's Classic Children's Books (published in softcover as The Classic American Children's Story: Novels of the Golden Age) explores how a large fraction of child-heroes in classic novels of the 19th and early 20th centuries are orphans, half-orphans, displaced from their homes, or have parental issues.
Every Anthony Horowitz series uses it, including Alex Rider, the Diamond Brothers series, the first 4 Gatekeepers in the Power of Five series, and the protagonist of The Devil and his Boy.
In Conn Iggulden's Emperor series, Brutus has a dead father and a mother who abandoned him in order to have a career as a higher class prostitute. He later finds a father figure in Renius, however he seems to prefer Caesar to Brutus, even dying to protect Caesar, which can be interpreted as one of the reasons why Brutus ended up turning on Caesar. After all, Caesar didn't need any further father figures, he already had his birth father and then his uncle Marius.
Jack Kerouac's poem "Home I'll Never Be" (which was also turned into a song by Tom Waits) is about a man finding his Disappeared Dad just in time to see him die of pleurisy.
By the Sword: The protagonist is orphaned by an attack at the beginning of the story.
Slightly subverted here. Yes her widowed father dies, but she meets her maternal grandmother for the first time in years and later finds out she has a clan of horse nomads for cousins.
To Take a Thief: Skif is an orphan who is technically a ward of his uncle as the story opens.
The Vows and Honor duology have this trope as backstory for both protagonists. The first short story, "Sword Sworn", opens with a bandit attack in which Tarma's clan is wiped out and she is left for dead. In the first book-length story, The Oathbound, we learn that Kethry's brother used his Promotion to Parent on the death of their widowed father to sell her into an Arranged Marriage. She was rescued and put into a Wizarding School.
Phoenix and Ashes: Since this is a World War I version of "Cinderella", this is a Justified Trope; the story opens when the now-orphaned protagonist learns of the death of her father, who was set up by her stepmother.
Serpent's Shadow: A Twice Told Tale version of "Snow White", in which the death of the protagonist's magician mother quickly led to the death of her father (since she had concealed him from a common enemy who objected to their marriage). The story opens after the protagonist has relocated to Victorian London in the hopes of escaping her family's enemy.
Gates of Sleep, a retelling of the "Sleeping Beauty" story, starts with Marina's parents agreeing to let Marina be raised by three of her godparents in secret.
Reserved for the Cat, Ninette's father disappeared when she was a baby, and her mother dies shortly before the novel starts. (Subverted when we learn Thomas the cat is Ninette's father, transformed when he lost a magic duel. He did what he could for his wife and child, but there just isn't that much a cat can do.)
Wizard of London, Nan doesn't know who her father is, and her neglectful mother eventually tries to sell her for drugs or alcohol. Luckily, Nan gets rescued by the boarding school that is giving her their leftover food.
Steadfast, Katie's parents die when their caravan somehow catches fire. In the ensuing grief, Katie is easily convinced by the owner of the circus her family worked for to marry the circus strongman, who turns out to be abusive.
Jaxom could also apply for this trope as well. His mother died in childbirth and his father, the evil overlord Lord Fax, was killed by F'lar in a fight over who ruled Ruatha Hold that very same day.
And also F'lar and F'nor, who lost their father in a duel at a very young age. Since Weyr children are fostered anyway, this might not apply.
Menolly's parents alternate between emotionally distant and abusive. Her father whips her back bloody with his belt. Her mother deliberately lets a wound heal half-crooked so that she has basic use of the hand but not enough to play an instrument. Small wonder that Menolly runs away to go live with the miniature dragons.
Joan Lowry Nixon's first few Orphan Train books dealt with six siblings whose widowed mother sent them out west for a better life. Most of the kids remain with their adoptive families even after she moves west herself and remarries.
The Crystal Gryphon: Joisan's parents died when she was very small, leaving her in the custody of her father's brother and sister. Kerovan was rejected by his Missing Mom at birth, so his Disappeared Dad fostered him well away from her.
Dread Companion: The protagonist was the product of a space Scout's Arranged Marriage, and grew up in a government creche without ever meeting either parent. (This is typical for Scouts.)
Lavender-Green Magic: When the kids' Disappeared Dad went missing in action in the Vietnam War, their Missing Mom had to take the best-paying nursing job she could get, which meant leaving the kids with her husband's parents.
Octagon Magic and Red Hart Magic: the female protagonist in each was being raised by her grandmother, who has become ill; she has now been turned over to an aunt. In the latter book, Nan's mother is alive but has a job requiring a lot of travel. (Red Hart Magic also features Chris, Nan's new stepbrother, who seems to have been putting up with his Disappeared Dad's job all his life.)
Both kids in the Star Ka'at books are orphaned; at the beginning of the first book, Jim was living with foster parents, while Elly Mae was living with her grandmother. Jim's foster home is a bit cool and unwelcoming to him, and Elly Mae's grandmother dies, so both children are not too sorry to leave Earth when offered the chance. They're told that Earth is imminently about to be destroyed in a nuclear war, and the Ka'ats (who've been disguised as domestic cats) are leaving; the two Ka'ats who befriended Jim and Elly Mae want to take them along.
Steel Magic: The three kids' parents are on a trip to Japan; the kids have been left with an uncle.
The X Factor: Diskan Fentress' mother suffered Death by Childbirth after his Disappeared Dad (a Scout) was sent out on an exploratory mission, leaving Diskan to be raised in a creche intended to train the next generation of Scouts - a job Diskan wasn't suited for. Subverted in that Renfry Fentress' return just prior to the opening of the story has turned the now-grown Diskan's life upside down.
Year of the Unicorn: Gillian doesn't remember her parents; she became a refugee at Norstead Abbey as a young child.
In His Dark Materials, Lyra Belacqua starts off the series being raised (for a given value of the term) by the faculty and staff of an Oxford college , believing herself to be an orphan whose parents died in an airship crash. Turns out they're both alive — her father is the man she'd been raised believing was her uncle, her mother is her malign Fairy Godmother equivalent — and they had a fairly solid reason for giving her up: not only was she conceived in adultery, her father had gone on to kill her mother's husband in a duel.
Will Parry. When we first meet him, he's forced to abandon his mentally ill mother who he's been taking care of from a young age to go on his quest. When he finally finds his Disappeared Dad, he's immediately killed.
Happens to many children in Citigazze. Their parents suffer Fate Worse Than Death by the Specters who suck out their souls.
Although Rowling kills parents and parental figures with merry abandon throughout the series, she also throws us an inversion: In Harry Potter and the Deathly Hallows, To protect her muggle parents, Hermione makes them abandon her by judicious use of memory charms to change their identities and make them forget they ever had a daughter. The emotional toll on her is quite intense.
Rowling not only admits to purposely orphaning Harry right off the bat, ("Harry had to be an orphan — so that he's a free agent, with no fear of letting down his parents, disappointing them....") but she even cites the Potters' brutal murder happening first thing in Harry Potter and the Philosopher's Stone to rebuff the argument by angry parents that her books betray their audience by getting progressively scarier.
NevilleLongbottom's parents didn't die either, but as one character puts it, "Better dead than what happened to them..." as they were tortured into permanent insanity by Death Eaters using the Cruciatus curse, and they don't recognise their son when he comes to visit. This is why he's raised by his domineering grandmother, who, on her first appearance, seems disappointed that Neville didn't turn out more like his dad.
Sirius Black was disowned by his Evil Matriarch mother when he was sixteen after he got sick of her Fantastic Racism. He promptly moved in with his best friend James and stayed until he was legally an adult.
Dean Thomas's father disappeared before Dean was born. Word of God says that Dean's father was a member of the Order of the Phoenix who was killed in the first war against Voldemort.
Sol's parents from Warrior Cats. Sol's father didn't like his mate, Cinders, or his kits; he rarely visited them, and brought them very little food. Eventually he ends up leaving them for a new mate who didn't complain as much as Cinders. Cinders, who never particularly liked her kits, ended up abandoning them at different Twoleg homes.
Somewhat obscure children's book The Divide has an interesting variation. Protagonist Felix is Trapped in Another World, but we do see how his parents are affected by his mysterious disappearance. They ain't happy.
Parents are not mentioned very much in The War Between The Pitiful Teachers And The Splendid Kids, seeing as the characters are in a prison-like school for bad teachers and smartasses. The lone(?) exception is Big Alice Eyesore, who was so wild as an infant (her teeth came in early; they were all canines) that her child psychologist parents left her in a wild animal park where she was raised by hyenas. They came back for her when she was an adolescent, but after learning that child psychology doesn't work on hyenas they abandoned her for good.
Bobby's family disappears in the first Pendragon book, and the only explanation given by Bobby's new father figure, Uncle Press, is that Bobby will see them again. The other Travelers with mentioned parents were raised by the generation of Travelers before them, who generally die somewhere in the series. An exception is Spader's mother, who disappears the same way Bobby's family did. Uncle Press kicks the bucket in The Lost City of Faar. However, he does come back in the last chapter of Raven Rise. Also in Raven Rise, several of the Travelers, who Bobby thinks of as his brothers or family, die. And then come back at the end magically along with Press. Mark and Courtney are assumed dead, though they turn out to be alive in the final book.
Animorphs features Tobias, who from the get-go is described as the abandoned child. His mother ran away and he never knew his father, though we do later find out that his father is actually Elfangor. Other than that, Marco also lacks a mother figure, as she apparently died a few years ago (though it turns out that she is Visser One's host). Jake also loses his parents when they become Controllers near the end of the series. On the flip side, some of the other members of the Animorphs force their parents to abandon them (similar to Hermione in Harry Potter above) to protect them from the Yeerks.
Tobias's foster parents, supposedly his aunt and uncle, also emotionally abandon him to the extent that he figures they won't bother to look for him when he loses his humanity.
The disappearance of Finn's parents is half the reason for the plot of the Finnegan Zwake books. (The other half is the murders that always seem to happen when Finn and his uncle go looking for them.)
Nobody in the Fingerprints series has both parents. Anthony and Jesse are missing their fathers; Rae, Yana, Mandy, and Emma are missing their mothers, and Sam lives on his own.
It's not that the Solo kids are abandoned by their parents; it's just that it's very busy work, saving and/or running the galaxy, hence their nanny, Winter Celchu, doing a lot of the work in actually raising them.
In The Chronicles of Narnia, the Pevensie childrens' parents rarely appear. Justified in that their father was drafted and their mother sent them to the countryside to escape the German bombing of London
In The Horse and His Boy Aravis' mother died much earlier in Aravis' life while her father tries to betroth her to a much older leader.
Many characters in J. R. R. Tolkien's The Lord of the Rings and The Silmarillion lost either one or both parents at an early age: Frodo (both his parents died in a boating accident), Aragorn (his father died when he was two), Túrin (his mother sent him away shortly after his father was captured by Morgoth), Tuor (his father died in battle before he was born and his mother died shortly after giving birth to him), Elrond and Elros (after they were captured in battle, their parents believed them dead and sailed away to obtain divine help) etc.
This may be because Tolkien himself was orphaned in childhood; his father died when he was four and his mother died when he was twelve.
In Megan Whalen Turner's Queen's Thief series, Gen's mother died when she fell from a building, as did his mentor grandfather. His father is still living, but as Gen is nearly an adult and in the employ of their queen, he doesn't need to involve himself much.
A more straight example is the magus of Sounis, who explains that his entire family died in an epidemic, and the queen of Attolia, whose mother died when she was young, considered of little importance most of her childhood, and whose father was perfectly happy to marry her off as a young girl to preserve peace in his troubled country.
In Dr. Seuss's famous children's book Horton Hatches the Egg, a bird named Mayzie gets Horton the elephant to sit on her egg while she takes a break... and then extends that break for months on end, without a care in the world. Eventually she shows up wanting the egg back, but then it hatches to reveal an "elephant-bird".
Angela Sommer-Bodenburg wrote a book of scary short stories with an injured boy named Freddy as a Framing Device. All five stories touch on Parental Abandonment. Barbara doesn't like it if you imply that her own death was her mother's fault. Harry drained his family's blood. The Child Under the Cloak was looking for someone to be her mother. Wolfgang has a father and step-mother who treat him like a freak just because he eats raw meat, howls at the moon and won't clip his nails. In the story Freddy writes himself, the Kindergarten class gets sick of their self-centered parents And They All Went Over The Hill.
Cynthia Voigt's Homecoming starts with the four child protagonists being abandoned by their mentally ill mother at a shopping mall.
In Gone , by Michael Grant, the entire cast is orphaned at the same time on the first page of the book, except possibly the ones with family living outside of the FAYZ.
Appears a lot in P. G. Wodehouse books. Bertie is an orphan who seems to have been largely raised by his aunts, and many of his friends seem to be in a similar situation. Psmith's father apparently died between books, leaving quite a few characters in the lurch financially speaking. Because it's Wodehouse, it's never really made angsty, though.
In the Chrestomanci books, Cat and Gwendolyn's parents are dead, Christopher's tend to ignore him, Conrad's mother is too busy writing to pay attention, and half the children in Witch Week have had one or both parents executed (and those that haven't have been sent away to boarding school because they are 'problem children').
In The Dalemark Quartet, Tanaqui and her siblings are left to fend for themselves, as are the children in Cart and Cwidder.
Mig's father in Black Maria has apparently been murdered.
Polly's parents in Fire and Hemlock divorce and toss her around between them until her grandmother takes her in.
Kathleen in Dogsbody is living with her aunt because her father is in prison.
Hailey's parents in The Game are presumed dead.
Maree and Nick in Deep Secret are half-siblings and children of the Emperor, but both are brought up away from him, as are all his children. Nick lives with his real mother, but she is killed at the end of the book, leaving him with his (thankfully not at all wicked) stepfather.
Abdullah in Castle in the Air dislikes his family and daydreams about finding that he is not really their child.
This tendency becomes a little unnerving once you learn how neglectful Diana Wynne Jones's parents were - the family in The Time of the Ghost is closely based on her own.
In On the Edge, the Draytons' mother first goes mad with grief and sleeps around indiscriminately, slowly dying inside. Then she finally does die. Later the Draytons' father runs off to hunt treasure, and when the novel opens he's been gone for several years with no word. Fortunately, Rose is old enough to raise her younger brothers on her own.
In The Wheel of Time series, Rand's mother died when he was very young, leaving his father to raise him on his own. In reality neither Tam nor Kari are his parents; his father was an Aiel and his mother was daughter-heir to the throne of Andor before running away to become a Maiden of the Spear. She died on Dragonmount shortly after his birth (thus setting the entire series in motion) and his father went to the Blight to fight and die to the Shadow after hearing of her death.
At the beginning of Andrey Lazarchuk's Tranquilium, the main character's father is dead and his mother, whom he never even knew, is in an insane asylum, because she is insane.
In Discworld novels, Rincewind doesn't know anything about his parents. He claims his mother ran away before he was born.
In Kingdom Keepers, Maybeck lives with his aunt Jelly. When Finn questions him on where his parents are, he only responds that they "aren't around," prompting Finn to drop the issue.
The second book reveals that Amanda and Jez live alone, having run away from their foster home.
He drove me from him at last, saying that I was but a common witch in spite of his teachings, and not fit to command the mighty sorcery he would have taught me. He would have made me queen of the world and ruled the nations through me, he said, but I was only a harlot of darkness. But what of it? I could never endure to seclude myself in a golden tower, and spend the long hours staring into a crystal globe, mumbling over incantations written on serpent's skin in the blood of virgins, poring over musty volumes in forgotten languages. He said I was but an earthly sprite, knowing naught of the deeper gulfs of cosmic sorcery. Well, this world contains all I desire—power, and pomp, and glittering pageantry, handsome men and soft women for my paramours and my slaves.
Inverted in Malevil. Emmanuel abandons his parents and is adopted by his favorite uncle. He considers his mother a simpering complainer, his father too cowardly to stand up to her, and both incapable of straight-forward honesty, leading him to run away from home.
Absolutely hammered in the once-popular ante-bellum girl's series Elsie Dinsmore. Elsie comes about after her father elopes with a beautiful young woman, who dies soon after her birth. The death causes her father to abandon his new daughter in his grief, so she is left with her grandparents, who vacillate between distant and abusive, who make her spend her days in the care of a tutor who also goes between distant and abusive. The only adult in Elsie's life who shows her any affection is her Mammy, but she doesn't really count, because she's not quite a person. When Elsie's father comes back when she's 8, he also ranges between distant and abusive, despite her pleas for his love and attention. Things finally come to a head where she meekly protests his plans to send her to Catholic school (because Catholics in general and nuns in particular are demons from hell), he abandons her, even giving a speech about how if she can't submit herself to his authority, she isn't fit to so much as be in the same house with him. He eventually comes back and they have a heartfelt reunion, becoming so close that she still sits on his knee and treats his word as law when she is a grandmother.
The children in Flowers in the Attic, LIKE WHOA. Not only does their father dying in a car accident set off the horrifying events to come, but they spend the rest of the book locked up in the attic of their grandparents' huge house with their mother showing less and less interest in their well-being while she attempts to reconcile with her dying father to try and get written back into his will. Meanwhile, during their confinement, their grandmother becomes more emotionally abusive towards the children because she believes them to be inherently evil. They are the product of incest.
And if you can believe it, it gets worse: When one of the younger children gets sick and dies, they figure out that their mother is trying to poison them so she can get remarried and start over with a 'clean slate'. Yeah...
Edgar & Ellen: The titular twins live alone on the edge of town, except for a scary, silent groundskeeper who they avoid. Their parents left years ago on an "around-the-world trip"—according to the note they left behind, anyway. The twins, left to their own devices, let the house deteriorate into a dirty, decrepit mess, go around in nothing but their pajamas, crawl around in junkyards and sewers, and terrorize the local populace. But given that they didn't even question their parents' disappearances until years later, we can probably assume they didn't have the best relationship anyway. The issue is mostly glossed over though, especially in the Lighter and Softer animated series.
In Sharon Creech's The Wanderer it is revealed that Sophies biological parents died when she was very little, after which she was passed from one bad foster family to the next, until being Happily Adopted. She forces herself to think of her current family as her only one.
In Jane Austen's Persuasion, it is casually mentioned that the reason that Captain Wentworth had stayed at his brother's and so originally met Anne was that his parents were dead.
In Gene Stratton Porter's Michael O'Halloran, Mickey's father died of drink, and then his mother, with no cause given. Near the opening of the story, he meets a crippled girl named Peaches, whose granny died and so will be taken to the Home.
Both Hagia and John go to fight in the Crusades in Dirge for Prester John, and neither of them seems to miss Sefalet that much.
At the beginning of the Outlander Leander series, Leander's father has been deployed. Since he was a single parent this leaves Leander in the house alone. He does, however, contact Leander daily, so he's only physically absent.
You may perhaps have been somewhat surprised, my Dearest Marianne, that in the Distress I then endured, destitute of any support, and unprovided with any Habitation, I should never once have remembered my Father and Mother or my paternal Cottage in the Vale of Uske. To account for the seeming forgetfullness I must inform you of a trifling circumstance concerning them which I have as yet never mentioned. The death of my Parents a few weeks after my Departure, is the circumstance I allude to. By their decease I became the lawfull Inheritress of their House and Fortune. But alas! the House had never been their own, and their Fortune had only been an Annuity on their own Lives. Such is the Depravity of the World!
Septimus: His parents are alive, but they usually don't show up frequently.
Jenna: Her father is almost always travelling around the world, and her mother is dead.
Merrin Meredith: His father drowned in the Castle moat, and his mother was confined to an Asylum, then fled to the Port.
In Palimpsest, Casimira was raised by her house after her parents leave her there.
In Alethea Kontis's Enchanted, they have had no contact with Monday since her wedding; Mama disapproves of receiving charity.
Farideh and her twin sister Havilar of Brimstone Angels were abandoned as infants outside the gates of a remote village. Exactly what happened there remains unclear, though it's later revealed that the twins are direct descendants of the infamous warlock Bryseis Kakistos (the eponymous Brimstone Angel) and its implied their parents weren't exactly model citizens either. Fortunately for them, they were Happily Adopted by Mehen and consider him their father regardless of biological relation.
Pippi Longstocking's mother was dead while her father was lost in the South Seas and didn't turn up again until the third book.
This happens to Benjamin in Never Wipe Tears Without Gloves. He's in his early twenties at the time but it's still noteable. He's a Jehovah's Witness who confesses to his parents that he is gay and in a loving relationship with a guy named Rasmus. A few days later his parents show up at his apartment with flowers and cake. During their visit Benjamin realizes that they are cutting all ties to him and that for all intents and purposes he's partaking in his own funeral.
Everyone else suffers from this. And I mean everyone. Jem even mentions that everyone is an orphan. To be fair, this is what the Institute is for. It's essentially an orphanage for Shadowhunters. If any of them had parents, they would be living with them. Except Will and later Cecily, whose parents don't count since they're not Shadowhunters.
In Andre Norton's Catseye, we learn in the first pages that Troy's father enlisted and never return, and his mother succumbed to the Big Cough.
In all three of Andre Norton's Warlock books, the main character is without parents. The death of Charis's father was the triggering of the opening events in Ordeal.
Candy's birth parents are killed in a traffic accident when she's ten months old. Her adoptive mother dies of an unspecified illness a few years before the events of the book, and her adoptive father is presumed dead after a bionuclear war, since he was in Washington, D.C., a known target for heavy bombing, at the time war broke out.
Adam's parents died in the epidemic triggered by said war.
Lisa's parents both survived the war and epidemic, but her father Jason was killed in an accident not very long after (mother Kim is still alive and a significant character herself).
In William Alexander's Goblin Secrets, all the children Graba took in have no connection to their parents. They don't even think of their mothers and fathers as Graba's children, though she calls them her grandchildren.
Happens rather commonly in The House of Night series if your parents don't approve of your new vamphood.
Zoey's mother has pretty much emotionally abandoned her in favour of her new husband/Church Militant religion by the start of the series anyway, and didn't need much more to abandon her child entirely.
This had also been happening to Aphrodite throughout the series for different reasons, but it was pretty much made official in Revealed, when her mother publicly disowned her shortly after the death of Aphrodite's father.
Sunny's mentor Sugar Cream in Akata Witch was found in the woods when she was three or so. She was found and raised by a seventeen-year-old.
The Mirrorworld Series: So, one day, Dad disappeared and Mom hit the sleeping pills... This is probably a huge contributing factor in Jacob's emotional detachment.
In The Shattered Kingdoms, Norlander culture believes in abandoning children who are deformed, and this happened to Lahlil (aka the Mongrel). She survives, and eventually returns. People who realise who she is tend to assume it's for revenge, but it isn't really (since the one responsible dies of illness anyway, as she knew he would). It's one of several things people incorrectly think she's motivated by.
Both Luis Black and Anna Maria Rosalita had mothers who died much earlier and fathers who died only about a year earlier or less.
Not uncommon in Dinoverse. Bertram's mother left the family for another man, and his father loves his work so much that he tends to forget Bertram, even though he's fond of his kid. Janine's dad died and she's increasingly distant from her mother, who never wants to talk to her - for a good reason.
The Osmerian Conflict Saku's parents are both believed dead from an accident prior to the start of the book, with Fae taking over as the parental substitute. Midway through the book his mother Arianna is revealed to be still alive, where she cites that due to her never wanting her son to join the military being at odds with the politically powerful UTSF she left him in order to give him a normal life.
The parents of the titular rascal boys in Max and Moritz are never seen nor mentioned. This is convenient, as it prevents the ending (in which the boys get killed) from becoming anything other than a comedy.
It's common for Dhampir's to have a Disappeared Dad, but Rose's mother dumped her at St. Vladimir's when she was 2 in order to continue her Guardian duties. Eventually averted, both Rose's mother and father begin to take a decent part in her life by Last Sacrifice. Her father more than her mother.