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At the end of Shadowchasers Torment, most of the villains are arrested or killed. However, the Three, the true rulers of the Cult of Tharizdun who orchestrated the whole plot, remain at large, and at the time of writing, have yet to appear again in the franchise.
It's assumed that most villains in Shadowchasers Ascension are horribly punished by Mephistopheles for disobeying orders, and a few are killed before the climax; however, Ibza not only gets away with everything he contributes to, he receives a promotion for remaining loyal and betraying his master's treachery. The heroes express how much the distorted politics of Hell sicken them.
Originally, Colonel Moran was going be this in Children of Time, despite the fact that he commits as many despicableacts as his boss, Professor Moriarty, does. In the end, however, the authors discovered that he really truly crossed the Moral Event Horizon several times over, and there was just no way it would be fair to the characters or to the audience to let him live.
Played with in the case of the plasmavore, however, who undergoes something of a High Heel-Face Turn. (She's an alien vampire and first entered the series by going on a killing spree throughout Paris, though out of the necessity of needing to feed on blood to survive, since she can starve to death.)
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, though he's at least reformed a bit by turning his talent for explosives into a lucrative fireworks business.
All things considered, Chrysalis turns out okay too, as she sets herself up as a beloved foal actress in Los Pegasus in order to replenish her power.
Nicely averted with Blueblood. After Chrysalis's 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 eluded capture ever since.
Zig-zagged in Vinyl and Octavia Duel Destiny. The main villain, Giovanni is killed at the end, but The Chessmaster gets away with everything they've done, with nopony even realising that they were behind the events of the past two fics.
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.
In The Adventure Through Runescape, the Demon Clan escape from prison and pull a Karma Houdini in the last few chapters of the story. The same also applies to the Big Bad's right-hand man, though this is meant to be a Sequel Hook.
Pretty much none of the major villains of Sonic X: Dark Chaos are punished for their actions. Tsali, and the Metarex leaders and Maledict himself join Sonic to fight Dark Tails during the final battle. Then Maledict pardons the heroes and leaves. Chris even lampshades it.
Chris: "Believe me, we'd love to beat you down for all the things you've done... but I think we're all just too happy it's finally over."