Used excessively and in a variety of ways in Avatar: The Last Airbender, due to the fact that war is raging. Aang, like all Airbender children, was raised communally by monks. However his father-like mentor, his unknown parents and the rest of his nation were entirely wiped out while Aang was frozen in an iceberg. Hence the subtitle of the show. Katara and Sokka's mother was killed when they were young and as of the beginning of the show their father has left to fight in the war. They live with their grandmother who rather blithely sends them off to travel the world with Aang (though it is later revealed that she ran away from home herself, which perhaps explains her attitude). Toph deliberately runs away from her overprotective parents. This trope even applies to Appa.
The villains have it no better. Zuko and Azula's mother Princess Ursa is absent (to say the least) and their father, definitely not the overprotective type, seems to have no problem with sending the kid he actually likes halfway across the known world to hunt his enemies. Zuko was banished on a Snipe Hunt (after being publicly disfigured and humiliated) for speaking out of turn when he was no older than fourteen. Mai's parents are seen briefly but seemingly have no interest or no say in her actions (possibly due to Azula's influence, though in "The Beach" Mai says that her mom repressed her a lot to not ruin Dad's high-profile political career) and Ty Lee's apparently did not notice when she ran away to join the circus, due to the 6 identical daughters.
Even the minor and one-shot characters suffer from this in spades — nearly every young person encountered by the main characters during their travels has lost at least one parent thanks to the ongoing war and its subsidiary disasters.
Played with for the main character who didn't live with her parents because once discovered as the Avatar, she was forced by the Order of the White Lotus to be cooped up and safely trained. But she did get to see her alive and well parents every now and then.
Mako and Bolin lost their parents to a firebender in a mugging, and Asami lost her mother to a firebender during a raid... this didn't go over well with her father, who is now dead to her.
Kuvira from Books 3 and 4. Unlike most of the examples above, in which the parent died or left for the sake of their child, Kuvira's parents flat out didn't want her and kicked her out when she was 8, resulting in her finding her way into the Beifong household. Predictably, this pretty much shaped her actions as the final Big Bad, seeing her nation being abandoned just like she was.
Charlotte from Making Fiends claims that her parents are in space, however, the series implies that her parents are dead.
It's strongly implied that Princess Bubblegum abandoned her son Lemongrab shortly after his birth because she couldn't handle the responsibility of raising a mentally unstable failed science experiment. According to Jesse Moynihan, a storyboard artist on the show, PB stuck him in a castle to be raised by servants. She acts like she's ashamed of his existence. This probably didn't do him much good.
In the flashbacks we see of Marceline's early childhood, her dad is nowhere to be seen. Made worse by the fact that she reallyneededaparent at the time. And she did find one in Simon Petrikov... but then he had to abandon her too, because his growing insanity was making him a danger to her.
At the end of season 5, Finn learns that his father is alive and is a prisoner in a crystal citadel. When we actually meet him at the beginning of season 6, he's less worried about making up for years away from his only son and more about escaping.
Xylene from Ben 10 explains her species, Uxorites, leave their children to fend for themselves as soon as they hatch, and as such cannot understand the concept of parenting in other species.
In Beavis And Butthead, their parents are sometimes mentioned but never seen, and they seem to take no real interest in the sometimes outrageous lives of their children. (In fact, the only who's ever mentioned with any regularity is Beavis' mother, who is said to be a slut; we find out in the film Beavis and Butt-Head Do America that the boys are the bastard sons of two heavy-metal roadies, and possibly half-brothers (Mike Judge refers to the two as their "dads", however).
Could be the dads are brothers, or half-brothers, making the guys cousins.
In Birdman, in the debut episode of Birdboy, Birdman's on-and-off sidekick, the lad is found separated from his father after an encounter with a supervillain. Birdman promises to help him find his father, but nothing ever comes of it. (His mother is never mentioned.)
Captain Planet and the Planeteers: Free room and board on Hope Island is part of the Benefits Package of being a Planeteer, so even the few parents who are still alive are mostly out of the picture.
Gadget from Chip 'n Dale Rescue Rangers lost her father a year before the team was formed. Due to lack of information, many fan theories exist about what actually happened. Her mother is never mentioned.
Parents in Dragon Booster are suspiciously absent, considering that their offspring are competing in dangerous sports with giant reptiles. Parm has a mother, mentioned once and never again, and Kitt has apparently left home or is an orphan (nothing is ever said about her parents). Only Artha (the protagonist) and Moordryd (his rival) have onscreen parents: Moordryd's dad is the Big Bad, while his mother, Zulay, is implied to be dead (the ambiguity of the line spawned numerous fanfics), while Artha has quite possibly the worst case of Parental Abandonment ever: his mother is never mentioned, while his dad, Connor, disappears in the first episode and is presumably dead... right up until the second season finale, when it is revealed that Mortis, who's been helping the heroes the whole time, is Connor in disguise. The reason for abandoning his children and letting them believe he was dead? They wouldn't have become independent.
In Ed, Edd n Eddy, we never see anyone at all in the show except for the children that live in the neighborhood. Sometimes parents and older siblings are alluded to, but they are never actually shown.
In The Oblongs episode, "Milo, Interrupted", it is revealed that Helga's parents left on vacation a year earlier and never came back... until the end of the episode, where it is revealed that they survived by eating the other passengers on the plane they took after it crashed.
Gargoyles: Tom, along with Princess Katherine, The Magus, Tom's mother, Mary, & Finella, fled from the castle of King Kenneth II when he was slain by Constantine, who later usurped his throne. After using the Grimorum to find a way into Avalon, The Magus is forced to give up the magical book because it can't be taken into Avalon. To keep it away from Constantine, so he won't be able to find them, Finella volunteers to protect the book and go into hiding from the King of Scotland. Mary volunteers to go with, deciding that protecting this magic book is more important than raising her only child, who at this point in the story wasn't even ten years old.
Demona didn't even try to stop the Magus and Katharine from "stealing" the eggs from the Wyvern Rookery, even though one of those eggs held her own child. In an unusual twist, the Magus and Katharine had in fact been entrusted with those eggs by Goliath, and they ultimately took better care of the eggs than Demona herself could have done, making this a rare positive example of this trope.
Dib and Gaz of Invader Zim have a father that is more concerned with his latest invention and his television show than whatever his children are doing, and a mother who is never mentioned (naturally, Epileptic Trees abound). Zim himself is a borderline example, as while technically he has no parents (Irkens are grown, not bred), his entire motivation is pleasing the parental figures of the entire species, the Tallest, who hate him and exile him to the far end of the known universe.
Jade from Jackie Chan Adventures is left by her parents in the first episode, and although they are alive, they are only referred to twice during the rest of the series. Jackie as well, it is implied, was sent to America to train with Uncle when he was a kid. His parents are never mentioned.
Paco's parents are never mentioned and it's possible they don't exist at all. El Toro, who is probably not his father serves as a father-like figure to the boy.
In Storm Hawks, the entire main cast is made up of 14-year-olds, and the show is one of the awkward cases in which nobody even mentions their parents. The closest we ever get is an aunt. And considering how many times they brush death, it's amazing they're allowed out of the house at all. (In fact, the only brothers we see freely admit to hatching out of eggs, leading to much speculation about how exactly the cast are born.)
In "Origins", Aerrow mentions that his, Finn's, and Piper's families and home terras were destroyed by Cyclonians. Stork mentioned an attack on his own terra, but nothing about his parents; Junko is similarly vague.
It is also heavily implied that Lightning Strike, the last leader of the original Storm Hawks, was Aerrow's father. Sure, Aerrow's only ever referred to as a "descendant", but considering Lightning Strike died in his twenties or thirties 10 years before the start of the series and Aerrow is 14...
In the cartoon Super Robot Monkey Team Hyperforce Go!, Chiro's parents have never even really been mentioned. If he had different caregivers than his parents, they aren't mentioned either. The kid just walks into a Super Robot, befriends some robot monkeys, and no parent/guardian seems to even care where he is. (Aside from the fan theory that Skeleton King may be Chiro's father.)
In the animated Teen Titans, the Titans are conspicuously independent, lacking even mentorsuperheroes (* cough* Batman * cough* ). However, many of their parents are actually accounted for: Robin's origin, although it is never covered in any detail, is hinted at in one episode and would dictate that his parents are dead. It also comes up a couple times in season four: Raven's mother appears briefly in one episode, and her father is a demonic overlord named Trigon (also evidently dead by the end of the season). It is also implied that Cyborg's parents and Beast Boy's parents have passed on, as well.
There's no excuse for Starfire though. In one episode they go back to her home planet, and are greeted by her "nanny". The rest of the episode involves Starfire's evil sister Blackfire usurping the throne and trying to marry Starfire off to stop a war. The fate of the original king and queen? Never mentioned.
The comic book, Teen Titans Go!, explained that they fell ill after their son (and Star and Black's brother), Wildfire, was sent off the planet and never recovered from it.
The Scooby-Doo gang members either have no parents or just very hands-off parents who don't seem to care that their teenagers go all around the world, hunting down villains in Halloween costumes. Subverted in the 'Mystery Inc.' series.
X-Men: Evolution is worthy of mention for its almost complete aversion of this trope. Despite living away from home, all the teens except Scott and Rogue have a loving family or foster-family to go home to in the obligatory Christmas episode. Kurt suffers from combined Missing Mom / Parental Betrayal, but still notes that his foster parents are great to him. The Brotherhood, on the other hand, have not fared as well — their parents are all absent for no apparent reason, Jerkasses, or the Big Bad (Quicksilver does seem to be treated pretty well, though, all things considered).
The titular bunnies from Yin Yang Yo have Master Yo the panda as their sensei and father figure, but so far their parents have not been mentioned... though some of their friends (and enemies) have parents ("CAAAAAAARL!").
It Was Later Revealed That Master Yo IS Yin and Yang's Father.
Inspector Gadget's niece Penny. He seems to be her only relative, although the backstory is pretty non-existent for her.
Implied in Ni Hao, Kai-Lan; Kai-lan's parents are never mentioned or addressed, even when other family members are featured.
The Boondocks: Huey and Riley's parents are never seen or mentioned, and it is not known how they came to live with Granddad. It's pretty heavily implied that they're dead.
Partially a case of All There in the Manual, or at least in the Comics. Their parents are dead, and in the first episode Granddad mentions spending their inheritance on that house (explaining in part why they were able to move to suburbia, hence, the boondocks).
Lance from Sym-Bionic Titan. His father supposedly died when he was very young, and he presumably had a Missing Mom, because custody was more or less given to the king and Modula, who sent him off to a military boarding school.
Some fans have noted that throughout the whole first two seasons, Vanessa seems to be the only child/teen character with two biological parents; everyone else seems to have a mom but no dad (or in Django's case, a dad but no mom). This recently changed when we finally saw Jeremy's father.
Doofenshmirz's parents couldn't even be bothered turning up for his birth.
In Max and Ruby, Ruby and Max's parents are never mentioned. They do have a grandmother. Possibly the only character with a parent that's seen in-show is baby Huffington, whose dad runs a shop in town.
In My Little Pony: Friendship Is Magic, Applejack, Big Macintosh, and Apple Bloom's parents are never seen, with their family matriarch, Granny Smith, acting as their guardian. While Applejack and Big Macintosh are at least old enough to live on their own (they stay on their farm due to the family business), Apple Bloom clearly isn't. Made even stranger seeing as the Apple family is the most detailed in the show. Word ofFaust and says that she and and her crew tried to come up with an explanation for where their parents were, with ideas such as them being travelling salesponies or simply being dead, but they never figured out what to do with them, so it's left ambiguous in the series.
Many fans thought the Season 3 episode "Apple Family Reunion", with a title like that, would finally shed light on the situation. It doesn't. There's a whole Continuity Cavalcade of every single Apple member seen in the series up to that point and even several new members, but if Applejack's parents were there they weren't identified. The closest we get is a pair of shooting stars that show up twice, which a storyboard artist has said is symbolic of their absence, which could mean a great many things.
No word on who Spike's biological parents are. All that's known is that his egg was in the care of Princess Celestia and was hatched by Twilight long before the series began.
After four seasons we have also yet to see Fluttershy's parents at all, even in flashbacks (Which focus on her time at flight camp) and they have never been mentioned.
Scootaloo has no known biological relatives to speak of either.
Rainbow Dash's implied parents are only seen in one flashback during "Games Ponies Play".
Daria Morgendorffer's home life is made more interesting due to her needy self-obsessed father - a man who lives in his own unhappy childhood and still has issues to resolve - and her workaholic mother who places job before family for the greater part of the time. This is one of the factors that shaped the Princess of Snark's alienation and mordant cynicism.
That is nothing compared to the home life of Jane Lane. There is a reason why there was a trope that was once called Casa Lane Parenting.
On Animaniacs, Skippy lives with his aunt with no mention of a mother or father. Years later, in an interview with The Nostalgia Critic, Slappy's VA Sherri Stoner claimed, in-character, that Skippy's parents dumped him on Slappy shortly after he was born, then left on a "sabbatical".
In Moral Orel, Joe's mother Nurse Bendy left him with his father, although he thought she died, as his father told him.
In The Smurfs, King Gerard's parents are notably absent from his life at the time he first appears as Prince Gerard in "The Clockwork Smurf". His aunt Imperia has taken care of Gerard, but desires to be coronated queen in her nephew's place, so she has him confined to the dungeon up until his twelfth birthday, where he will be Released to Elsewhere...a plan that was foiled by the arrival of Clockwork Smurf.
In Gravity Falls, Soos' dad left him when he was very young and never visited, only sending postcards. His grandmother reassures him that he'll visit someday, but in some (Spanish) lines she says to herself, it's clear she thinks the father is a terrible person. As for his mother, we never see her.