None of this was mine any more ... I was followed by a darkness of which this world of home knew nothing. How many secrets I had had, how often I had been afraid — but all of it had been child's play compared with what I brought home with me today. I was haunted by misfortune, it was reaching out toward me so that not even my mother could protect me, since she was not even allowed to know.
Double Subverted in the Harley Quinn series - the child in question was already pretty jaded, having been hunted by crooks her whole life, but hanging out with Harley she almost got her innocence and faith in the world back from being with her... until Harley's conscience fails and she cashes in the kid anyway. Ironically, after the villains take what they want from her (her eyes), the now blind girl has a feeling of peace for the world and a new lease on life (and nothing but pity for the crooks that used to come after her), while Harley is completely unable to look herself in the mirror.
X-23's origin story is even called Innocence Lost, as it depicts in disturbing detail the pain and suffering intentionally inflicted on her by the Facility to strip her of her humanity and turn her into an emotionless killing machine. Although they failed, the emotional damage that was done to her was still severe. Laura continually struggles to form relationships with others, and her desire to find a life as something other than a weapon and killer is an ongoing theme for her character.
In Kung Fu, Caine remembers a time when he was tricked out of a precious scroll by a con man. Eventually, the con man is caught and the scroll is recovered, but Master Po and Caine have a disappointed conversation that ends with:
Caine: But Master, the scroll was returned! Master Po: But your innocence, how will that be returned?
Subverted in Mork and Mindy when Mork is talked into freeing an escaped criminal who claims that he just needs to visit his sick mother and will return to turn himself back in afterward. Sure enough, Mork is arrested for freeing him and Mindy tells him that it is obvious that the crook took advantage of him and won't be back. In a genuinely moving moment, Mork tearfully agrees that he can't trust anyone again, until the crook suddenly returns as promised to turn himself in and get Mork released. With that, Mork's innocence is restored with his naive belief in the goodness of humanity vindicated.
On 3rd Rock from the Sun, Dick responded like this to getting mugged. He had tried to politely explain to the mugger how "this three hundred dollars is mine" and when that didn't work, he ended up losing his faith in humanity for the rest of the episode: "What kind of place is this where you can't wave handfuls of money around in the middle of the night?"
This is referenced in the original Peter Pan; It's noted that every time Peter is exploited (e.g., by Captain Hook) or similar, he reacts with shock and the typical apparent sting of the loss of innocence, but he continues to fall prey to these tactics because he never will actually 'grow up' enough to lose this childish na´vetÚ altogether. He also forgets traumatic events magically, so that he never matures via suffering.
A subversion of this is a major plot point in the Amber trilogy in Dragonlance. To destroy the Beloved of Chemosh, they must be physically touched by an innocent child. The experience is so horrific, said child will lose their innocence, making dealing with them a Sadistic Choice for the good guys.
An important theme in A Song of Ice and Fire, with the whole "Winter is coming" theme. Especially important in the storylines of Arya and Sansa, who both start the series fairly deluded but very quickly lose any delusions they might have, in addition to more or less having any part of their old personality beaten out of them. The result is a somewhat manipulative and highly deceptive Sansa and a full-on child soldier Arya.
Frodo goes through this in the The Lord of the Rings. The burden of the Ring alone is enough to drive him to despair and make it difficult for him to return to the peace of the Shire. Add the pain of his injuries (the Witch-king's knife, Shelob's sting, and losing his finger) and the suffering he endured on the journey, and it becomes impossible, prompting him to depart into the West to be healed.
Lolita. Despite portraying Dolores Haze as a Fille Fatale, Humbert Humbert realises by the end of the book that he has destroyed her childhood.
The quest that starts the Dark Brotherhood questline in The Elder Scrolls V: Skyrim is actually called "Innocence Lost". The innocent children in question get a double helping of this. Their innocence has already been shot to Oblivion by being orphaned and sent to Riften's Honorhall Orphanage where the very ironically-named Grelod the Kind makes their lives a living hell. Aventus Aretino flees the Orphanage and tries to contact the Dark Brotherhood through the Black Sacrament (using his own dead mother's remains) to kill Grelod. What's left of the orphans' innocence dies a nasty death when you kill Grelod, since you show them that Murder Is the Best Solution. Aventus even tells you that he wants to be an assassin like you when he grows up so he can "help" people too.
Pretty much the entire point of Tomb Raider is to show Lara's innocence being forcibly stripped away by her experiences on the island in one long Break the Cutie moment. Unlocking the model gallery even calls Lara's pre-shipwreck model "Innocent Lara."
Fallout: New Vegas has the Dead Horses. Honest Hearts has you decide whether you should defend Zion Valley following Joshua Graham at the cost of their innocence, or protecting it by following Daniel and helping them escape the valley.
Played literally in the Christmas special of The Amazing World of Gumball. When Nicole tells the kids that Santa isn't real, an aura of multicolored light, representing their innocence, escapes their bodies through their mouths.