Little Orphan Annie. She soon had a very strong father figure in Daddy Warbucks, but the earliest stories had her on her own in the world, and she never really has a mother figure.
Except in Annie, the stage musical adaptation and the film musical, where she has Warbucks' secretary Grace acting as a mother figure.
The title character in the newspaper strip Dondi was an Italian WW 2 orphan adopted by an American GI, although this was de-emphasized after the strip's first few years.
Wellington in the British newspaper strip The Perishers is an orphan who lives with his dog Boot, originally in a large concrete pipe and later in a small abandoned railway station.
Runaways — Look at the title! Their parents aren't curiously absent so much as a group of supervillains out to help evil supernatural beings destroy the world. How's that for family issues?
In Spider-Man, young Peter Parker lives with his aunt and uncle because his parents were killed long before the story opens, in most versions before he was old enough to remember them. His parents' death usually has little to do with his origin story, that role going to Uncle Ben.
One doesn't necessarily think of Batman as having Parental Abandonment issues, mostly because he's not a teen hero and, unlike Spider-Man, never was, but it is worth noting that he his parents were killed right in front of him when he was a child, and thus he was able to spend most of his teen years taking about 20 levels in badass.
Tim Drake (Robin III), who previously only had a case of missing mom, becomes a full-fledged orphan in the Identity Crisis mini. Made all the more poignant in that he and Batman hear the whole thing over the phone while in the Batmobile, interspersed with the son of his father's murderer, Captain Boomerang listening to, in effect, a suicide message from Captain Boomerang. The whole sequence ends with a very heart-wrenching two-page splash of Batman cradling Robin in his arms over his father's body.
Dick Grayson (Robin I) and Jason Todd (Pre-Crisis) were both orphans from their origin stories onwards.
Other examples in Batman are Jason Todd (Post-Crisis; Robin II), whose long-lost mother betrayed him to the Joker and was killed in the same explosion that killed him, Cassandra Cain (Batgirl III), whose abandonment by her mother was part of the bargain between her parents to turn Cassandra into the perfect killing machine, and arguably Stephanie Brown (Spoiler), whose villain father was in jail for most of her childhood and who threatened to kill her should she act against his plans. Oh, and Kate Kane (Batwoman), whose mother was murdered when she was a kid.
Damian Wayne hadn't met his father until recently. That changed when Batman "died".*
He was displaced in time by Darkseid's Omega Beam to gather more Omega energy
And since he chose his father and Dick Grayson's ideals over his mother's, Talia has abandoned him also.
In the X-Men titles, the teenaged mutants of Xavier's School are a mix of orphans, those with families hundreds or thousands of miles away, kids actively rejected by their parents, those on the run from parents who wish them harm, and other similar abandonment issues (for example, Kitty Pryde's parents went into the witness protection program (her father has since been killed). And Rogue's mother, it turns out, ascended to a higher plane of existence.)
Applies to the adult members, too. Classic examples include: school founder Professor Xavier (father, mother, and stepfather all died before he was out of his teens), Cyclops (parents threw him and his little brother out of a burning plane with the only parachute as young children), and Storm (grew up a Street Urchin after a plane crashed atop her family home, killing her parents and burying her alive).
In most continuities Xavier himself is a less than stellar father. It's especially blatant in Ultimate X-Men. He abandoned his family to work for mutant rights with Magneto, and barely gave his son a second thought. When Magneto (not a great father himself) called him out on this, Xavier justified it by claiming that he and his son had nothing in common so the boy wouldn't miss him. Xavier really believed that his son wouldn't suffer abandonment issues just because they didn't have common interests.
In most continuities, though it varies widely with the writer, Xavier is a very shady character in general. A very slight change in the angle through which you view him can make him look very much like a villain, using vulnerable and damaged teens and young adults as pawns in his own obsessions and contributing to the very problem he claims to be trying to solve. He's a very ambiguous character.
Magda fled from the man who would become Magneto and disappeared (she is usually believed to be dead), it was only many decades later that Magneto learned that she had been pregnant with Quicksilver and the Scarlet Witch.
Gabrielle Haller did not tell Charles Xavier that he had impregnated her and for decades he believed that her son Legion had been fathered by a mutual friend. Similarly, it is indicated that Nereel's son Peter was fathered in the Savage Land by Colossus, only she never confronted him with that.
Nightcrawler's and his half-brother Graydon Creed's abandonment by Mystique may be among the worst examples from the series.
DC's Teen Titans are prone to this as well — at one point in the '80s, they had exactly one member with biological parents who weren't dead, evil, or on another planet/dimension (possibly in an effort to keep up, in the first couple years of his own book his father turned out to be evil and then committed a Heroic Sacrifice, although it was reversed a few years later.) Changeling went through four different parental figures (not counting the ones who were evil) and eventually wound up with a stepfather who spent a significant amount of time going missing and/or insane. And he was still one of the most attentive parents in the book.
Skywise in ElfQuest. In a backstory episode it is revealed that two teenage humans who only wanted to prove their manhood by playing a prank on the "demon" elves accidentally started a chain of tragic events that led to his parents' deaths, but not before his mother had set the newborn Skywise adrift on a river. He was found on the riverbank by the other elves and raised by the entire tribe.
Cutter loses his parents as a young teenager. His mother is killed (along with several other elves) by the monster Madcoil, and his father dies trying to take revenge. Cutter then organizes the rest of the tribe to avenge all of the deaths by killing the monster.
Superman has had it both ways. His origin has always involved the destruction of his homeworld, and his birth parents along with it. As for his foster parents....
Silver Age Superboy stories made much of the tragedy of Krypton, to the point where Superboy always referred to the Kents as his "foster parents".
A major element of the Post CrisisRetcon was that Ma and Pa Kent were still alive and well; Jonathan has since died, but Martha is still alive and well.
A major inspiration for the Smallville series was an avid Superman fan describing to the producers that Superman is unique to comics because his parents being there for him when he was a young child growing up with the powers of a god made him the man he is today. Early seasons of Smallville averted this trope many times and has been argued to be more about Jonathan and Martha raising the world's greatest hero rather than about Clark. Then they left the show and it leaped tall sharks in a single bound.
Superman's clone, Superboy (Connor Kent), is close to one of his fathers, but the other rarely if ever has anything to do with him, other than occasionally trying to use him as a weapon against the father Connor is close to.
Tintin is especially impressive, because with the exception of the Thom(p)son brothers (who are only pretending to be twins, being unrelated lookalikes), and one fleeting reference to Captain Haddock's mother, it would appear that no one in the series has any relatives whatsoever. Whenever Tintin runs into kids, they are orphans. And no one, but no one, falls in love or gets married or is portrayed as being married. Pure True Companions.
Averted in a few cases with supporting characters: The Maharaja of Gajpajama and his son appear in The Cigars of the Pharaoh and The Blue Lotus; in the latter story, Mr. Wang heads a happy family with his wife and son Didi, and later adopts orphaned Chang, and the gypsy girl in The Castafiore Emerald has family too (this story also shows Calculus being shyly enamoured with Bianca Castafiore). However, the other examples are not so sympathetic: bratty Abdallah is spoiled rotten by his doting father, General Alcazar is paired with a harridan of a wife in Tintin and the Picaros, and then there is the horrible petit-bourgeois, "Belgican" Wagg clan...
Completely averted with Blue Beetle. Jaime Reyes' parents are both not only alive, but are very involved with his life as both a teenager and superhero. Plus, they're made of 100% pure awesome.
Played straight with his friend Brenda, whose mother died of an illness and whose father was murdered by her aunt after he beat Brenda badly enough to put her in a coma.
Though they're adults in the series, most of John Byrne's team Alpha Flight have parental abandonment issues. In particular, the twins Northstar and Aurora are orphans, and didn't even know each other until adulthood.
Dr. Jack Hack of Hack/Slash left his wife and child due to a combination of gambling debt and being on the run from government agents because He Knows Too Much. His wife, Delilah, turned out be a cannibalisticSerial Killer who killed herself upon being discovered by the police, rose from the dead, and had to be re-killed by her own daughter. All this happened before said daughter, Cassandra, turned 16. No wonder Cassie is so screwed up.
For Wild Children like Tarzan to be raised by animals (or gods or spirits or whatever), their parents have to be missing or deceased. This also happens to Nävis (in the French Comic BookSillage, a.k.a. Wake) — the only survivor of a spaceship crash, raised by a robot and a tiger; and also to the eponymous Pyrénée from another French comic, raised by a bear after her mother dies in an earthquake; and to numerous other characters. The Other Wiki has a list, but it's probably far from comprehensive.
Bruce Banner's parents were both dead by the time of his accident with the gamma bomb.
For context, his parents were dead because his father killed his mother when he was a child, and he killed his father in "self defense".
His sidekick, Rick Jones, was also an orphan.
As for the Hulk's sons, Skaar and Hiro-Kala, their mother died in an explosion, and their father, unaware that they had survived their mother's death, headed back to Earth to seek revenge on those he blamed. Neither of them is entirely happy with their father.
His daughter was also raised without him because her mother (Thundra) took his DNA to the future to impregnate herself with it. She wasn't around for a good bit of Lyra's adolescent years herself. Banner also has another potential daughter running around, but they haven't officially confirmed the relationship yet.
Subverted with Battle Guy in Kick-Ass 2 - his origin story is that his parents were killed on the way home from the opera, and the criminal then forced him to watch as he cooked and ate his parents, then spent all the father's money on pay-per-view porn. However, Dave recognizes the voice of his friend, Marty Eisenberg, whose parents are alive and well; turns out he just thought superheroism would be fun, but (mistakenly) believed Justice Forever wouldn't accept him unless he had a cool background.
Green Arrow's sidekick, Roy Harper/Speedy, was adopted by the Navajo after his forest ranger father died in a fire. He was then raised by a Navajo medicine man until he died as well. Then he was adopted by Ollie, who was so inattentive he needed Hal Jordan to attract his attention to Roy's drug problem, and reacted by throwing him out of the house. (You might notice everyone in this story is male; much later, Roy would claim "I don't have a mother. I don't even have a story about having a mother.")
The Destine family in ClanDestine. The two youngest kids are raised by an older brother and sister (who pass as their uncle and grandmother; it's complicated). Their father spends their first decade of life in space in a state of Heroic BSOD; their mother has been off in a sort of Alternate Dimension, and it's hinted that she can't leave it, period. At any rate, older siblings raising younger ones seems to be the usual pattern for the Destines, rather than an emergency measure- one of the adult siblings mentions that he was also raised by an older brother, despite the fact that their father at least would have been on the planet at the time.
The Falcon and his siblings lost his preacher father, killed trying to break up a fight, when he was a teen. Two years later, his mother was shot and killed by a mugger.
Disney comics has this in tons. Every child of any importance seems to be living with their aunt or uncle. Huey, Dewey and Louie, in particular, whose parents have scarcely been mentioned since Donalds sister dropped them off at his house and drove off with only a note that their father was in the hospital, after the boys put a firecracker under his chair, and asking Donald to take care of them for a bit. That was in 1937. Daisy also has three nieces, Mickey Mouse has two nephews and Goofy has one. DuckTales gives us Webby, who lives with her grandmother. In each case, their parents go practically unmentioned, despite Goofy otherwise having a large extended family.
In WITCH, Will Vandom started out this way. Her parents divorced when she was young because her dad was a compulsive gambler. When he did come back, it was only to squeeze more money out of her mom. Years later, she did get a stepfather in the form of her teacher. As well, Irma Lair has a stepmother and stepbrother, but nothing is said about her mom or her stepbrother's dad.
The cartoon, though, alters this, making Will's father extremely less of a Jerk Ass and turning Irma's mother and brother into paternal family.
Sonic the Hedgehog is this in spades. Name a character. Chances are that they went parentless or are missing a parent or two. Of the main Freedom Fighters, only Antoine and Bunnie are parentless after the initial war with Robotnik. The Chaotix aren't so fortunate - nothing is mentioned of Vector's family or Espio's father, Mighty and Ray's parents are MIA, Julie-Su's parents were killed by her stepsiblings, Charmy's presumably died when Eggman attacked Mobius after Sonic's disappearnce and Knuckles' parents got divorced with his father performing a Heroic Sacrifice to save him.