Death Note Equestria has Ace and Colgate discuss this trope at one point: The Kira Neutrality Movement's plan to remove Kira's motivation to kill — by being harsher on criminals — doesn't take into account a way to actually capture Kira, letting her get off scott free with mass murder. Ace finds this an acceptable loss; Colgate disagrees.
The Hasbroverse turns Cobra Commander into one — according to a blog post by the author, when Serpentor had Cobra attack the Decepticons, the Commander panicked, grabbed as many bank books/PIN numbers as he could, hopped on a hydrofoil with a handful of loyal soldiers (who probably count too by extension), and fled Cobra Island. Because of this, he not only escaped the resulting massacre, but now lives like a king in upstate New York.
In The Prayer Warriors, which features Percy Jackson, Harry Potter and the Carter Kane Chronicles, Voldemort, despite being both an enemy to the Prayer Warriors and Hogwarts, is forgotten about after one attempt to blackmail Draco into killing Michael by threatening to kill Ebony. So far, the Prayer Warriors have also succeeded at killing everyone who disagrees with them; while they suffer casualties in the process, their dead quickly return to life, and any defeats they face are typically, at worst for them, mere setbacks.
In Perfection Is Overrated, The Advisor/The Avatar, who created the SUEs (each of whom has tried to kill the Himes and reshape the world as they see fit), never answers for his actions, although Natsuki does (unsuccessfully) try to kill him. The Avatar points out that the sense of futility they feel in trying to make him answer for his actions is the same experienced by those who try to go up against a Mary Sue who, unlike the SUEs, is not on a relatively level playing field with the canon cast.
Earth and Sky: The Flim-Flam brothers' Sycophantic Servant Otto Bomb, who willingly aided them in all their illegal activities in the story, eventually ditches them after they decide to continue the Pegalthon even after being disqualified and ordered arrested. Despite a run in with the Royal Guard, Otto evades capture and is last seen living comfortably in Mexicolt with a beautiful mare.
All things considered, Chrysalis turns out okay too, as she sets herself up as a beloved foal actor in Las Pegasus in order to replenish her power.
Nicely averted with Blueblood. After Chrysalis impersonation of his wife is foiled, it at first looks like he'll be free of consequences from his role in that and his hateful marriage... for about two minutes, until Fancypants shows up and begins his Humiliation Conga.
Related, the PER are almost never punished, despite being terrorists who forcibly ponify innocent civilians.
Subverted in the Deconstruction FicThe Conversion Bureau Not Alone: To wit, Celestia purposefully transported Equestria to Earth with the intention of transforming all of humanity into ponies while also wiping out any trace of their existence under the guise of a diplomatic mission, destroyed several human cities with the barrier, left millions of people displaced and homeless, and was directly responsible for starting a war that cost the lives of several soldiers on both sides. When she realizes humanity is going to win, she takes Equestria and retreats, leaving more than 3000 Equestrian ponies and 800 Newfoals behind to an uncertain future on Earth. The subversion arrives in the final scene of the story, where it's revealed that the combination of losing the war, missing their friends and family members they left behind on Earth, and the weird behaviors of the Newfoals has caused several ponies to start questioning Celestia's actions and lose their faith in her, and moreover, the zebra and gryphon kingdoms are not happy to hear about what the Princesses tried to do, with the Gryphon Queen herself telling Celestia in a letter that her Omniscient Morality License has been revoked and she will have to answer for her crimes eventually.
In The Nuptialverse, it's established that, unlike canon, Trixie didn't have a Heel Realization after the events of "Magic Duel". Instead, still left half-mad by the Alicorn Amulet, she flees into the Everfree Forest, where she's alluded capture ever since.
Rayquaza a.k.a. The Ghost King in Latias Journey. He starts the story by massacring everyone in Altomare note Since Altomare is a Venic Expy, probably around 800,000 people, because Latias turned down his romantic gestures, and then attempts to murder her crush. He eventually apologizes, not because he murdered so many people, but because he made Latias upset. That said, she not only forgives the Ghost King, but also reciprocates his love by only halfway through the story. The author gives a justification that it was just Kyogre's subconscious suggestions that made Rayquaza do it, but this falls apart since comes at the end of the whole story, meaning Latias had forgiven and romanced him when she believed him to be responsible.