A Different Medius has Buwaro deal with his entire hometown being destroyed by horrorterrors, and being unable to find his adoptive dads as well as finding out that your adoptive Dad happens to be the reason your biological parents are dead to begin with. Holy shit.
Better Angels drives the nail home that Shane Walsh, who has survived his battle with Rick, is a sociopath who would murder his best friend in cold blood. While consoling his dead friend's son, he knows he has to make his cover story convincing by being emotional, but can't bring out any real tears over his dead friend. Instead, he envisions his friend's wife, who he also has deep feelings for, being eaten alive by her reanimated newborn during childbirth.
Blind gives us this scenario. It's the night Hinata's 3rd bithday and everyone is asleep. Cue Hinata's mother (Hinati) hearing a 3 year old Naruto (adopted son) screaming. Hiashi chuckles and says it's just Naruto being Naruto. Hinati says she's going to check on both Naruto and Hinata. She comes back crying saying they're missing. Oh but it gets worse. Hinati immediately chases after Naruto's screams and eventually catches up to the kids in the forest. What she sees is Hinata lying in a pool of blood with empty eye sockets. She turns about to throw up only to see Naruto pinned to a tree by kunai, 1 of which is through his heart. You guess her reaction.
A The Lord of the Rings fic Elladan's Trials For Estel deals with a young Aragorn (who was adopted and raised by Elrond) being kidnapped from Elrond's bedroom and Buried Alive. One chapter writes from the perspective of the kidnapper and it turns out the kidnapper worked and lived in Rivendell. It didn't help when the kidnapper mentioned there were some nights where he would stand over a sleeping Aragorn, thinking how easy it would be to kill the boy while no one would know.
Delw Yomenie Deadly Encounter has Elrond and his warriors going to rescue the kidnapped Aragorn and during the ambush Elrond released an arrow to kill just as the kidnapper shoved Aragorn to the frontline. That split second when he realized his hand would kill his adopted son, Elrond was torn between denial and horror. Fortunately the arrow hit a non-lethal area.
In The Roots of Evil, Elrond helplessly watches as his sons Aragorn, Elrohir and Elladan are slowly dying from a poison to which there is no antidote.
Elladan: "I do not fear the poison, ada."
Elrond: "But I do, ion nin, I do."
Aragorn feels guilty because he had indirectly caused his brothers to be poisoned when a madman wanted to get his revenge on him and his brothers were simply there. Elrohir comforts him, even though they both know they may not survive the poison.
And with that, Elrohir drew his brother into a hug, holding him tightly, wishing that the things would be as easy as they once used to be, when Aragorn's hurts could have been cured with a smile, a kiss and a hug.
In Final Section, a Supernatural fic, five-year-old Sam Winchester was taken by a man who preys upon children in a school's playground when John happened to be preoccupied, despite attentively watching Sam. The detail that the assailant had already kidnapped several other children by luring them away from their watchful parents (and being gleeful about his successes) was disturbing.
In Harvester Of Eyes, John Winchester is pitted against The Corinthian. The fact that he's hunting a possibly-human monster who preys on young boys, while having to keep track of his two young sons on the road, aside... Sam and Dean get lost in the Dreaming on their own. Dean obviously knows enough about pedophiles, creeps and "stranger danger" to be on high alert regarding anyone who might hurt Sam, he can't get it across to him that sometimes the really dangerous people can look perfectly normal. Even cool and fun to hang out with.
Past Sins has one marking the point where everything goes down the tubes...namely, a child being forcibly taken away from their guardian, who can do nothing to stop it. And then said child believing their guardian wanted to give them away.
In Progress, Sundance and every other pregnant mare in Equestria are worried for their unborn foals after the Discord incident.
In Detective Conan fic When Pandoras Box Is Opened, when Conan was kidnapped by Vermouth and everyone panics. Those who know the kidnapper have even more reason to fear because the Black Organization has no problem indoctrinating young children into complete loyalty to the organization. Jodie has a brief vision of an older, ruthless Conan preparing to kill a victim and is appropriately horrified.
There is a scene during The Tamers Forever Series where the pregnant Mimi Tachigawa is kidnapped and taken to a laboratory where her unborn child is forcibly extracted from her. She is then left to wander the wilderness as her grief slowly drives her insane.
In Streets Of Rage Saga, based on the Streets of Rage beat-em-up game series, two incidents are related in the back-story some twenty years before the story's modern-day timeline, both of them involving children: an infant was snatched when his parents looked away for just a moment and he was later murdered, and some time after that a girl wandered away from her parents along a beach and was attacked by the same perpetrator moments later. What makes it even more horrifying is the common nature of both incidents—both were committed by a feral child.
The Axis Powers Hetalia fanfic Power Shift has this example: Tino or Berwald, or even Francis'. They fear their child has seemingly disappeared into thin air. You feel as though something bad can and will happen to him. And in Tino and Berwald's case, it turns out they're right.
There's also the fate of Estonia, especially the chapter describing what happened leading up to it. It really plays on the fear of a family member being abducted and having something horrible happening to them.
In another Hetalia fic, Human Curiosity, nearly all of the world's nations disappear. They just vanish, leaving their friends and family panicked and traumatized. This goes on for a century, leading to most of the remaining nations to assume that their loved ones are never coming back. And then, they learn that not only were the nations kidnapped and tortured for that entire century, but a lot of them were horrifically murdered and frozen in blocks of ice. There's a bit where America, Germany, and Japan get to explore the kidnappers' base, while being terrified and trying to guess who was and wasn't killed. Oh, and the surviving nations were all completely insane when they were found, to the point where they couldn't even recognize their rescuers as people.
Raven's Tears: Native America is forced to watch as she slowly loses control of her own land. Then, she realizes that the shift in ownership of the land is represented through her sons, who morph from being Native American children to having blond hair, blue eyes, and being only able to speak French and English. And after all of this, Native America has no choice but to give them to the nations invading her, because she can't communicate with her own children.
Feverish starts with the basic premise of Canada getting sick with something. Not so bad at first, with him getting a fever and feeling nauseous. Then, he starts hallucinating, passing out, and suffering increasingly dangerous side effects. All of this goes on while America, France, and England are trying to take care of him and make him better. There's one chapter where Canada gets a nose bleed so bad that England thinks someone was attacked in the room. He attempts to stop the bleeding, only for Canada to go into respiratory arrest. Throughout this, no one knows exactly what Canada is sick with, which means they have no clue as to how to heal him. And on Canada's side, it turns out his government is forgetting about him. So there's the fear of being completely forgotten and neglected going on.
Awakening has two big hitters. The first is on France and England's side. Imagine your younger brothers go off to fight in a war and disappear for a long while, only to show back up dead, mutilated, and infected with disease. America and Canada get better, but still France and England have to go through it all. The second is what happens to the other children, most of whom never survived, despite America and Canada's best efforts.
The Weakest Link: America, England, Norway, Denmark, Russia, Finland, Sweden, Poland, and Lithuania are Forced to Watch as sociopathic scientists torture Sealand, Estonia, Latvia, and Iceland in the name of 'science'. Made worse as Fletcher's almost pedophiliacal obsession with Latvia forces the adults to worry that he might end up being raped and the others will be forced to watch.
In the Sherlockian Deliver Us From Evil Series, Inspector Lestrade fears for the safety of the young Baker Street Irregulars. Considering that he's friends with at least one, has another among his constables, and has a nephew in their ranks, he's very close to them and has every right to feel a parental horror at the boys putting themselves In Harm's Way.
Later on, Dr. Watsondisbands the Irregulars when one of the very young ones is nearly killed.
Silent Hill 2 fic Coming Home is a cornucopia of this; with James's father Frank Sunderland having to watch his son spiral into depression and starts acting erratically after his wife's death. Frank find out that James is being stalked by a powerful force that is obsessed with him after he didn't believe his son's fears that something was out to get him. Frank finds it would do anything to possess him and outright threatens sexual violence on James to Frank. After his son goes Silent Hill, Frank never sees his son again.
In Marie D Suesse And The Mystery New Pirate Age, toward the end, it is revealed that the tragic events that occurred for the last 20 years in the One Piece world can be undone, but if Madelyn never ate her Devil Fruit, she would never have made the mistake of causing Luffy's execution, fled to the "real world," changed her name to Blake, met Garreth and had Marie. Not only are Garreth and Madelyn/Blake aware that they'll never see each other or their daughter again, but Marie realizes that she'll be erased from existence entirely, and feels as though her existence was a mistake.
In Cosmic Warriors shortly after Naru is raped the man appears in Usagi's school and is later spotted chatting with Makoto. Nothing like having your children attend a school with a rapist on the grounds.
In Kyon Big Damn Hero, Akane was taking care of a feverish Nonoko, her daughter, who was hit by a cold and left her alone in her room for a few minutes and upon her return Nonoko was nowhere to be found. When phone called later she was told that the girl was in fact kidnapped, but thankfully she was already rescued by her brother. This also applies to her husband Yuuto who was left in an Heroic BSOD by the news of his daughter missing until he was informed Nonoko was safe.
In Symbiosis, Professor Oak relied on his former reputation to keep Pallet Town safe. Instead his student, Delia and her family were murdered in the middle of the night of a criminal organization and their corpses had to be identified by their DNA.
In Pokémon False Red, Red's mother has to deal with her son's disappearance when he went training and receives no closure on whether or not her son's dead.
In Turnabout Nephew, the young son of Ema and Klavier ends up meeting Kristoph Gavin in solitary confinement, after getting lost from his mother. While Kristoph shows no inclination to hurt the boy, given what he already tried to do to people in the game (including to a little girl), it's easy to see why Ema and Klavier are so scared when they find out.
Street Sharks Redux was basically the original series rewritten to be Darker and Edgier and make more prominent the Fridge Horror of the show. As a result, the story doesn't shy away from creepiness like one's family member vanishing, finding oneself forced to hide from the community, living in fear of being kidnapped and hurt, and so on.
The final story of Calvin & Hobbes: The Series, "Black Rain", has Socrates almost being kidnapped by a strange man in a masknote heavily implied to be Masky from Marble Hornets, which makes sense given that Slender Man himself is in the storywho'd invaded his mansion. Things only get worse when it's revealed he had a knife the whole time and is still in his house. Then Socrates points out that he could still be around when Elliot (his owner, a young boy) and his family return...
The admins of The Infinite Loops have prevented anybody caught in the eponymous time loops from having children since they know full well any such children would cease to exist once a loop resets.
In Apollo Justice: Ace Attorney fanfic Dirty Sympathy, Apollo and Klavier deal with being trapped in abusive relationships with people who have the skills and connections to make their deaths look accidental. Especially since Apollo is reminded by Kristoph that if he goes missing no one would know since Apollo doesn't have any family or friends.
Mass Effect's fanfic Crucible is a giant list of all the horrible things could happen to your child. From the Bad Future to the present timeline, it can say that almost every character has experience this in some forms:
The whole chapter where Garrus and his dad have to investigate the missing cases of the pregnant mothers carried hybrid children. Their men are trying to find them with (almost) no hope. The governments from both sides don't give a damn about them. Meanwhile, the people around them keep mocking/harassing them for being xenophiles. Not to mention the women were kidnapped so the Quarians can do tests on them and turn their children into slaves.
Your son from a bad future hates you for what your alternate self did and no matter how much you love him and tries to prove it to him, he keeps rejecting you. Poor Garrus has it bad.
In the Bad Future, Garrus, to drown his sorrow of losing Shepard, had sex with Perdita (the recon scout) and accidentally knocked her up, forced to marry her only to discover that Shepard was still alive and also very pregnant. Their son ended up being born as a bastard. Then the child got molested by his step-mother (who was also a victim of Parental Incest herself) while Garrus was absented and scarred for life. To make things worse, Shepard got killed and Garrus was forced by his father-in-law to abandon Gaius (or the bastard would kill the child) and the boy got shipped off to a place where people torture and forcing his kind to kill. If you think things would get better for the child once Sidonis saved him, you're dead wrong.
Also in the bad future, Miranda managed to have a child that she was also wanted but he was taken away from her to be a test subject why she was imprisoned. She got away with Tiberius but could only live with him for a few short years before her past caught up and she has to lead them away to keep her son safe.
Shepard's pregnancy is basically an Adult Fear fuel for Garrus (or any Turian with a pregnant partner).
Shepard is in her labor and a strange turian kidnapped her, made his wife do something to the child inside her (Shepard) and she couldn't do anything to stop it.
Your child being born too soon and you thought he would die from it.
You left your kid with a babysitter to go out for a bit. You felt worry, run back home, found the babysitter injured on the floor, the crib is empty, and you knew who did it. Even God couldn't save Tali from Garrus's wrath now.
The comrade that had fought against death with you had betrayed you by kidnapping your son. And this was after you didn't confront her about her first sort-of-betrayal.
In Diaries of a Madman, Shining Armor mistakes Cadance's scream of frustration while playing video games as her being under attack.
"Fluttershys Night Out" is a rather dark My Little Pony: Friendship Is Magic story. In it, a (teenaged and very innocent) Fluttershy does not get attacked by monsters or subjected to any supernatural menace. Nope. Instead she goes out to a pub in the hope of making friends and is wined, seduced, used and abandoned by a smooth-talking stallion, who does so simply because he wants sex and she's naive enough to think he loves her. Oh, and this happens before she's made a lot of friends (this would be during the period when Rainbow Dash was away and Rarity was Fluttershy's only social contact) so she by implication has no one to help her and responds to the experience by blaming herself, assuming that she's inferior to other ponies, and becoming the half-crazy hermit who Twilight Sparkle eventually encounters in My Little Pony: Friendship Is Magic S1 E1 "Mare in the Moon". In other words, she's an emotional wreck for years to come. And yes, the scenario is quite plausible, even in as nice a society as Equestria's.
In Gensokyo 20 XX, we have this played definitely straight in both Gensokyo 20XX and 20XXI in that the thought of having Reimu, Yukari's surrogate offspring, all alone without in a time where she could run the risk of being apprehended or the fact that she may be apprehended and possibly executed and, in the second one, being Ran being separated from her offspring and not knowing will happen to them.
In chapter 12 in Gensokyo 20XXII, Ran finding out two of three of her babies have died not too long after being forcibly separated from her and Reimu is being doped up by force with tranquilizers every three hours for screaming, as well as the fact that is and was virtually powerless to stop it.
In Reimu's Illness, the thought of your child dying from multiple potentially fatal illness
In 20XXIV, in chapter 9 with Reimu crawling off, right into danger, and, later on, in chapter 28, we have Chen who is attacked no sooner than when she goes outside and the resulting attack leaves her with her left arm and leg paralyzed from nerve damage and incontinent. What makes either of them worse is the former was conditioned not to sense danger and the latter because someone/thing was lying in wait when they attacked Chen and it was going for the kill.
Also from 20XXIV, We have Chen attempting suicide
In 20XXV, we have Reimu almost dying after consuming rat poison and, later on, we have Reimu, Renko, Sanae, An, and Youmu getting out of the apartment building and only An being found, the others being lost in a world they could be killed, traded, or eaten. To worsen, the latter, one of the kids is near blind. Fortunately, they were found in a forest.
Also from 20XXV, what a poltergeist does with Reimu, that is, spiriting her away. Of course, this really blows a head when she is spirited away from her crib whilst she is asleep and it was like she was barely there and they do not find her until after the poltergeists are vanquished. Also, one of said poltergeists is attacking the children, even to the point of almost killing them (the first time is when Yume Ni was scratched on the neck and it came very close to killing her if not rendering her unable to talk and, the second time, the children are chased out while she is throwing things at them, one of which being a table).
In Sly Wits Paradise, Luna risked getting trampled by a herd of frightened earth ponies if she fell from Whip Scar's back and Celestia found herself in the middle of a clearing when a hunting griffin is hovering above her. In the next chapter, a pack of hungry wolves went after the foals of the herd.
IN Shatterheart Fai is on a rare outing with Syaoran, joining him at a bookstore during the Infinity Arc. Syaoran takes off by himself to get some air and gets kidnapped by a bunch of thugs and is tortured by serial killers for their amusement. Fai and Kurogane run themselves ragged trying to find him and pray that they find him in time.
In Kill la Kill AU, we have a then six-year old Ragyo being hit by a car. In that vein, Nui being dragged down into the basement by whatever was down there.
In the Star Trek: The Original Series fanfic Insontis, in "A Considerable Lack of Amusement", McCoy is drugged unconscious and the de-aged Kirk is kidnapped in the middle of a crowded amusement park. The best Spock can hope is that Kirk was taken as a hostage and not something nastier.