The Confessor is purposefully torturing himself by using a cross as his costume theme, as a form of mortification in penance for his killings as well as his self-loathing as a vampire.
Eth, the narrator of "Sorrowsday".
"I can live with it no longer. I surrender to your justice. What is my punishment?"
The Street Angel becomes this after turning Darker and Edgier during his time with Black Velvet; in remorse, he left Astro City to do humanitarian work in Africa, before returning to the city to help inner-city youths.
In "Mistakes", Marella Cowper becomes this after she overlooks a clue to a hidden Skullcrusher base in Ecuador, turning the area into a war zone. She leaves home and devotes herself to aiding rescue efforts in a desperate attempt to find the child who originally contacted her, getting into more and more dangerous situations as a result.
The title character of Atavar, despite not ever actually being a villain, becomes one anyway after being tricked into dooming the Kalen.
In Chaos! Comics, Mary Young works to make up for how her self-serving experiment caused the undead serial killer Evil Ernie's creation by looking for ways to stop him and helping refugees from the Zombie Apocalypse as a doctor. Dr. Leonard Pierce tries to be this, but because he's obsessed with killing Ernie no matter what and even at the cost of the people around him he usually just makes things much, much worse.
Crimson: Ekimus is the last surviving member of the Grigori, a soulless race that sided with Satan during the War on Heaven and was completely exterminated. He had forsaken the forces of Hell in shame and tried to atone for his crimes. Unfortunately he ended up crossing paths with Lisseth and together, they created the vampire race that would plague mankind for eons to come. Ekimus would spend his following days searching for a chosen one to help him destroy all vampires.
Rayek from ElfQuest tried to Set Right What Once Went Wrong, nearly wiping out everyone and everything he cared about in the process. He spends much of the rest of his eternal life trying to make up for this.
Sistah Spooky (who is not a villain, but can be pretty bitchy) becomes this in Empowered #4.
The Lost Boy: Walter decides that he needs to make up for everything he did as The Vespertine.
The Mandy story "Sorry Sue" has this premise—Janie, the heroine has been mean to foster-girl Sue and now regrets her actions, so she is trying (unsuccessfully) to make amends.
Rat Queens has Sawyer, a former criminal turned captain of the guard of Palisade. When he's tortured for past crimes he accepts it fatalistically.
Shakara: Dr. Lara Procopio has tried to make up for her role in engineering the disease that was used to destroy the Shakara race through humanitarian missions and dedicating the rest of her life to helping the sick and wounded. When Shakara the Avenger comes to execute her, she admits that it's not meant to excuse what she did and chooses to Face Death with Dignity.
Skull Island: The Birth of Kong: At the end of this MonsterVerse graphic novel, Aaron Brooks becomes this. Having kicked off the entire plot of the graphic novel which led to the deaths of everyone else on his expedition and multiple casualties for the Iwi, he opts to stay on Skull Island a while longer and doesn't even ask for any rescue in the log he sends out to sea, feeling he needs to help make up for the mess he made.
Knuckles was like this for a bit after his time as the new Enerjak.
Heel Face Turned villain Dimitri also feels the need to atone for his previous deeds, and issue #221 has a touching moment between him, NICOLE and Espio, both of whom are also invoking this trope following their respectiveactions during the Iron Dominion arc.
Hope Kintobor does this as well. She had stayed at Knothole until, at the advice of Snively, wandered off to explore the world. When she came back, she found out that Knothole was razed completely and she thought that the Mobians there were dead. Though she later found out they were alive and well, she felt horrible for listening to Snively's advice and, as such, allied herself with G.U.N. and Team Dark to get back at the former Kintobors, vowing to make their name worth something in the end.
Sally is hit with this in the post Sonic the Hedgehog/Mega Man: Worlds Collide universe when she finds out what she did as Mecha Sally. NICOLE and Cream have to convince her not to go total workaholic on them.
Spawn. Especially since it was revealed that he chose to come back as a monster because that's how he viewed himself in life.
A few characters in Vampirella were presented this way:
Her mother Lilith was the original wife of Adam who had spawned countless races of demons and monsters upon the world after refusing her role. Seeking to redeem herself, she gave birth to Vampi and trained her to fight monsters in hopes of her hunting down evil. Turns out it was a subversion, she was not really atoning for anything, but planning to take over Hell using the dark essence of all demons her daughter killed. Lilith was using her daughter all along to gain power while using an atoner facade.
Pantha used to be an Ax-Crazy cannibal that was worshipped as the goddess Sehkmet and killed children in cold blood. She was cursed by the gods for her cruelty by being transformed into an immortal shapeshifter that could transform into a panther. She tries to atone for her atrocities by fighting evil, but she occasionally suffers memory loss because of the same curse.
In a very early story, Dracula attempted to become this trope. In this continuity, the events of the Bram Stoker novel (where he killed Lucy Westenra and nearly turned Mina Harker) were real and with the help of Vampirella and Lilith, he traveled back in time to stop himself from doing either. When it seems he is successful, he ends up faltering and murders both Lucy and Mina.
Mosely of Mosely volunteered to help the military create the AI that took over the world. He deeply regretted it.
