Captain America: Bucky Barnes was brainwashed into a Russian assassin known as the Winter Soldier. When he gets his memories back, he is full of guilt over the things he did. His first solo series makes his atonement a focal point by having him go after Russian sleeper agents he had helped train in the past.
Deadpool: Deadpool is trying to atone, but the fact that he's so bad at it, combined with his natural psychopathy, means that most people don't even notice.
Hawkeye: After being manipulated to villainy, Hawkeye joined the Avengers as a way to both make up for what he did, and also to do what he originally intended to do with his skills: Help people.
Moon Knight: Moon Knight fights crime in part to make up for the evil that he did as Marc Spector while fighting with Bushman's band of mercenaries. Since he is, Depending on the Writer, a jerkass, insane or both, these attempts can get complicated.
New Warriors: Post-Civil War (2006)Speedball is blamed for 612 people he didn't actually murder. Even so, he changed his name to Penance and designed a costume with 612 points of constant pain. It turns out that he didn't make the suit for himself—he made it for Nitro, the true murderer. He only wore it because he felt he had to atone somewhat for failing to save all those people. Eventually, Speedball finally got some professional help and returned largely back to normal.
She-Hulk: In She-Hulk (2004) Vol. 2 #4, Jen works as a volunteer for Green Cross, a Hero Insurance organization dedicated to cleaning up the damage caused by the Hulk and other gamma-radiation cases. The Green Cross leader and founder later reveals that he was the one who dared Rick Jones to sneak into the gamma-bomb testing area, so he feels responsible for the very creation of the Hulk.
Spider-Man: Peter Parker gained amazing abilities after being bitten by a radioactive spider, and immediately tried to use them for his own benefit. One night, he failed to use his powers to stop a thief from escaping, and flippantly brushed off the people who protested that he easily could have intervened; it wasn't his problem, why should he? Unfortunately, later that night his beloved uncle — who had always tried to teach him that "with great power Comes Great Responsibility" — was murdered, and after pursuing the culprit in vengeance the boy was horrified to discover that it was the same thief he had let escape. Devastated by guilt, the boy from that day resolved to use his powers to atone for his inaction by using them to fight crime as the Amazing Spider-Man.
After several attempts to take over the universe, Thanos of Titan may have become the Atoner. In Marvel: The End, he destroys himself or seems to to save the universe, and then in a self-titled series started wandering around atoning for his old deeds. No one trusted his motives and the series was canceled before it was truly clear how genuine his motives were.
Thunderbolts: Songbird honestly saw the team as a chance to redeem herself. Too bad the Thunderbolts were reorganized to be little more than killers on a leash after Norman Osborne took over.
Similar, Flash Thompson, Venom IV, in the new series. A former high school bully who tormented many students during his teens (of which including Peter Parker and Jessica Jones), he was inspired by Spider-Man to turn his life around by joining the army. When he lost his legs in Iraq, he then signed on to become a Government-sponsored secret superhero using the Venom Symbiote. A lot of his motivation comes from wanting to make up for being such a horrible person during his teens.
Ultimate Vision: Tarleton added Gah Lak Tus technology into his own body, but ended up working as his agent instead. Vision restored his sanity. He accepted that he made a big mistake, and helped to defeat Gah Lak Tus from then on.
Wolverine confided to Spider-Man that he puts himself through agonizing punishment after punishment as penance for all the terrible things he can remember and not remember doing in his past.
The Destruction of Tian is something that Kitty regrets, to the point that she willingly stepped down from her leadership of Utopia.
Following Avengers vs. X-Men, Scott Summers, who under the corruption of the Phoenix Force caused the death of Charles Xavier, was willing to spend the rest of his life in jail paying for that and any other crimes he committed under its control (for those who don't know, that basically amounts to him refusing to do what the Avengers told him to do), until he realized that the sudden burst of new mutants mean that a large number of people are going to be hunted down by anti-mutant extremists, so he decided to break out of prison to protect them. Now, still hunted by the government and his former teammates, he's formed a new Brotherhood of Mutants so he can track down new mutants who need protection, whatever it takes. Most, however, just assume he's off his rocker and trying to upstage humanity. Though, he probably doesn't help his case by calling it a 'mutant revolution', or with the fact that his powers are on the fritz, making him unintentionally far more dangerous than he intends to be.
Gambit joined the X-Men due to the whole unwittingly helping the Marauders commit the Mutant Massacre. Admittedly Gambit never intentionally took part in said massacre and continues to be a much-loved thief with a heart of gold to fans, but still.
Magneto seems to go through regular cycles of Big Bad, Well-Intentioned Extremist, and The Atoner. During one of his atonement phases, he even joined the X-Men.
Sabretooth is a big example. As a villain, he committed almost every crime one could think of. He's been an assassin, abuser, serial killer, mass murderer, cannibal, and possibly a rapist. His good & evil side are inverted during AXIS and he becomes a good person, trying to atone for all his past sins — vowing to Logan that he would find his own Wolverine spirit.
Leads into Reformed, but Rejected seeing as no hero in Marvel fully trusts him. After the Axis storyline ended, Creed acknowledged that many would only ever see him for the beast he was. So he's prepared for everyone's slights toward him, but he still gets annoyed with it.
