Gary's daughter, Chloe, in The Astounding Wolf-Man. She begins totally supporting her father, then when she finds out he's Wolf-Man, she freaks and doesn't trust him, and after she slowly starts trusting him again, she thinks she witnesses him kill her mother. After this point, she becomes a villain in the series, also thanks to being misled by a former ally Zechariah, who had his own Heel–Face Turn. Eventually, Gary convinces his daughter of what really happened, and Chloe returns to his side.
In Avatar: The Last Airbender - The Promise, Zuko seems to be courting an alignment switch (again) from his status at the end of Avatar: The Last Airbender, to which the comic is a sequel. The eponymous promise was made to Zuko by Aang, swearing to take him down if he ever started acting like his father. Throughout the comic, he becomes more and more obsessed with protecting his people and the many assassination attempts he's undergone, and the last panel of the first volume has him seeking advice from his father in prison. And we know that he makes yet anotherHeel–Face Turn by the end, since The Legend of Korra info has already confirmed he and Aang found United Republic together.
Darkwing Duck has Mortimer L. Marquand. When he first appears, he's the super-villain Cat-Tankerous. When he appears in the next volume, he's reformed his ways, only to eventually want to go back to villainy, attempting to join forces with Negaduck. But then that turns out to be an act and he's a face again. As of the book's cancellation, he's appeared to settle on heel for good by teaming up with Darkwing's old enemy Fluffy.
In the G.I. Joe comic published by Marvel, Storm Shadow was initially conceived as a mere mercenary hired by Cobra. When his back-story revealed that he was a former student of the same Ninja master that trained Snake-Eyes, he underwent a story arc which involved a reconciliation between himself and his former sword brother. He eventually left Cobra and sided with the G.I. Joe team, going as far as to lead their "Ninja Force" division. During the end of the Marvel run, Storm Shadow was brainwashed into serving Cobra again. The brainwashing was never meant to be permanent, but the comic was canceled before the story arc could be resolved. When the comic was renewed by Devil's Due Publishing years later, Storm Shadow was still employed by Cobra for quite a few issues until he was finally free of his brainwashing and rejoined the Joes for the remainder of the series until the Continuity Reboot.
In The Golden Age, the criminal Tigress did a Heel–Face Turn when Tex Thompson gave her amnesty for her crimes, and became a hero until her lover Lance Gallant was killed in a Heroic Sacrifice fighting against Robotman. After that, she turned back to doing crime.
The Madballs comic book published by Star Comics (a subsidiary of Marvel that was dissolved in 1991) had the villain Anchor Man. After making his debut as a villain in the fourth issue, he appears a couple of times as a normal newscaster, with the eighth issue even having him explicitly say that he is reformed. This is apparently undone in the comic's ninth issue, where he resumes the identity of Anchor Man and works together with several other enemies of the Madballs.
The Mickey Mouse Comic Universe has Professors Ecks, Doublex, and Triplex, a trio of monkey mad scientists who menaced Mickey Mouse and Horace Horsecollar in the Floyd Gottfredson comic strip story "Blaggard Castle". At the end of the original story, Mickey used the mad scientists' own hypno-ray against them and hypnotized them into becoming good guys, but later comics featuring them would have them become evil again. Two different explanations were given. One was in the 1993 Disney Adventures story "Return to Blaggard Castle". While the Professors themselves didn't appear, the Phantom Blot disguised himself as Professor Triplex and at the end of the story explained to Mickey that while the hypno-ray reformed the scientists, it did not keep them sane, which resulted in them ending up in jail, where they told the Blot about their encounter with Mickey Mouse. The other explanation for the Professors becoming villains again was given in a 1995 comic strip story featuring Ecks and Doublex, where they revealed that they returned to their evil selves because they were hit by water balloons and getting wet undid the effects of the hypno-ray.
Geoffrey St. John is a prime example of one of these. It's even Lampshaded in one issues' off-panel strip.
Rouge was even worse. One story taking place in a single day featured her switching sides at least five times.
Snively practically wears this trope in the Pre-SGW era. He has worked with Robotnik and Eggman against the Freedom Fighters, switched to the Freedom Fighters against Eggman, switch to Eggman (again) and worked with The Iron Queen against the Freedom Fighters, and eventually turned against Eggman for himself.
Star Wars IDW: Spock's father, Sarek, in the "Vulcan's Vengeance" arc. He initially joins the Narada survivors in their attempt to obtain Red Matter and destroy Romulus, but finally gets his bearings after his son discovers him while undercover, and helps them foil the plot.
From Star Wars Expanded Universe, Quinlan Vos, a major character in the Star Wars: Republic comic books, is a good example. Here's how he progresses:
First appears as in the Malastare arc as a minor character who operates most efficiently from the shadows, but is nonetheless a respected Jedi Knight (that's good).
Next, he shows up as the main focus of the Twilight arc. Having suffered a complete mindwipe, he's no longer inhibited by the Jedi teachings and resorts to using the dark side to find his missing apprentice (that's bad). At the end of the story, he realises his mistake and submits himself to Mace Windu for retraining (that's good).
Saves the Republic in the Infinity Gate arc (that's good) and gets his knighthood back as a result. Then there's the Darkness arc, which sees him resorting to the dark side once again to fight mutant space vampires (that's bad), but he's able to get himself together again in time to defeat Volfe Karkko (that's good). The next arc which has him as the main character doesn't really feature much of his struggle with the dark side.
Then there's the Clone Wars stories, which Adapted Out Vos' previous stories and characterization but still sees him getting involved in a tangled web of byzantine plans enacted by himself, his Master Tholme and Count Dooku. To become The Mole in Dooku's gang of dark Jedi, Vos fakes a defection to the Separatists (neither good nor bad), killing the information broker who betrayed him in the process (that's bad). While he's there, he proceeds to kill both his Evil Matriarch aunt (who organised the murder of his parents) and a corrupt senator after being convinced by Dooku that he was Darth Sidious, injuring another Jedi Master in the process (that's bad).
After killing several more on Dooku's orders - having decided that Dark Is Not Evil and convinced himself that his victims would endanger the Republic otherwise (that's bad) - he meets up with his childhood friend, Obi-Wan Kenobi and rejoins the Jedi Order (that's good). However, it seems that he's actually spying for Dooku (that's bad).
Finally appears to resolve his problems once and for all in the climactic Saleucami arc, which shows him defeat the dark Jedi Master Sora Bulq, save the life of Master Tholme and pledge to leave the Jedi to marry his love interest Khaleen after the war was over and raise their child (that's good).
But it's not done yet. Quinlan's final story is set during Order 66, which shows him deciding that he has to survive and kill Emperor Palpatine by any means necessary (that's bad). Ultimately, though, he realizes that his duty as a Jedi is to protect a Wookiee village from the clone commander hunting him, and seems to sacrifice his life to stop him (that's good). He survives, returns to his surviving friends and promises never to let his darkness affect his infant son (that's even better). So, there we have Quinlan Vos; possibly the only Star Wars character even more conflicted than Anakin Skywalker.
Luke Skywalker in Dark Empire can't compete with Vos, but he does manage to emulate his dad. First, he confronts the Emperor Reborn. Then he realizes that he can't win and joins him, planning to subvert the Empire from within. Then he falls to The Dark Side for real, having very Sith thoughts about killing his Master as soon as he's learned enough — when Leia and Han come to try and rescue him, he captures them and chokes Han. Then, Leia talks him into seeing the error of his ways, so he helps them escape with some important codes before trying to kill Palpatine. Palpatine beat him and bent him back into line — Sith apparently don't mind attempted murder that much, it's kind of expected — and Luke served him and regretted letting his sister go. Finally, he met Leia again, who redeemed him into realizing that he didn't want what Palpatine taught, he wanted to be a Jedi.
There's also Baron Soontir Fel. He never was shown as a really bad guy, but he switched sides like few others. Let's see — the best Imperial pilot barring Vader (and that's debatable), and receiver of a baronial title, he became quickly disillusioned with Empire and joined Rogue Squadron in exchange to help in searching for his wife, then involuntarily left the New Republic (he was abducted) for a stint in the Empire of the Hand, then served the Chiss Ascendancy (again distinguishing himself there up to receiving the Assistant Syndic position), and then returning to the Empire again, now serving Pellaeon's Imperial Remnant... Let's say that when his children founded a new Empire, it didn't surprise anyone. However, his Hegemonic Empire was actually a good one for once, aligned to the Light and greatly improved the galactic citizenry's quality of life... until the Sith ruined everything again.
The Tomb of Dracula: Depending on the Writer, Lilith can fluctuate between protecting the innocent with no ulterior motive to building an army of zombie slaves for nefarious purposes.
