A rarer occurrence which is in some ways the inverse of Anti-Hero Substitute, this is a Comic Book trope wherein one holder of a certain identity (usually a Legacy Character) is a hero despite all other versions of that character being villains. Sometimes the character taking on this persona will speak of a desire to "redeem" that identity, especially if they are a child of the villainous wearer of the costume. Arguably, this trope happens for similar reasons as the Anti-Hero Substitute. The Anti-Hero Substitute aims to makes a hero "cooler" by having a character with the hero's powers but less restraint in using them. In a similar way, Evil Is Cool, and this trope allows villain powers to be showcased, but by a character with heroic aims.
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In a way, Dark Schneider in Bastard!! is one of these. The original Dark Schneider was pretty much an Evil Overlord, but then was sealed in a young boy. Thanks to the goodness of the "container", while the new Dark Schneider has the personality of the original (a lecherous egomaniac), he is a saint compared to the original.
This is largely Sai Akuto's goal in Ichiban Ushiro No Daimaou. Of course, it's rather hard to win the trust of the people when the Sorting Hat vocational raven says that you're going to be a Demon King. Things aren't as white and black as they seems.
In Spider-Man, Phil Urich stumbled on a Green Goblin costume and got doused in the Super Serum (note, it was explicitly this — unlike the earlier Psycho Serum, this one didn't make you insane), producing the irony of a guy a lot like Peter Parker (snarky journalist Unlucky Everydude) taking on the identity of Peter's worst enemy. In the main Spider-Man series, Urich did end up suffering from mental problems and ultimately pulled a Face-Heel Turn.
In the Spider-Girl series, things went better, and he is an Honorary Uncle to the heroine, and has moonlighted as a superhero in both his Green Goblin costume and as the "Golden Goblin" (basically a Palette Swap Hobgoblin).
Also in the Spider Girl series is Normie Osborn. Following his father and grandfather, he took on the Green Goblin identity as a villain, but after conquering his demons ended up being a Redeeming Replacement for Venom (although he doesn't call himself that)- he was forcibly merged with the symbiote but managed to stay mostly sane with it and fight crime. Similarly to the irony with Urich, Normie is a friend and love interest to May Parker, despite running around in the costume of one of her father' worst enemies.
And, the series has another example in Brenda Drago, Raptor, who ends up marrying Normie Osborn. She's the daughter of Blackie Drago, the second Vulture and started out as a criminal, but then reformed and became an antihero.
Back in the main Marvel Universe, the Venom symbiote is now a US military asset, and the man in the suit is Flash Thompson, who took the job because it was a chance to be Spider-Man.
The versions of Sabretooth and Mimic that were members of the Exiles were heroes from alternate realities. However, the original Mimic isn't so bad these days.
While on his deathbed, B-List supervillain the Black Knight begged his nephew Dane Whitman to restore honor to their family legacy and to atone for his crimes. Whitman did so, becoming a heroic Black Knight still active to this day. The villainous Black Knight is also something of an inversion: he based the identity and his equipment off of his heroic ancestor, the medieval Black Knight.
One version of Toyman is a young Japanese genius, while the other versions of the character are all villains. Unfortunately he, like all other versions, turned out to be a super-advanced android, created by the one and only original Toyman.
The Red Hood, which is generally told as being an identity of The Joker before he became a Monster Clown. The identity is also used by some of the Robins, mainly Jason Todd, typically when acting as anti-heroes.
The female Dr. Light, who (like the Toyman example above) is a Japanese genius. She's also a Hot Scientist and Mama Bear - as opposed to the first Dr. Light, who was a man, a villain, and a rapist (by retcon).
This is the basic idea behind Brainiac 5 of the Legion of Super-Heroes, descendant of Superman villain Brainiac. (There are intervening Brainiacs of varied morality, but they weren't really focused on until well after B5 had been introduced.)
Also from the Legion, Danielle Foccart assumed the codename "Computo" in the V4 era when she gained Technopathic powers — after the villainous AI that possessed her in her first appearance (her brother Jacques' origin as the second Invisible Kid).
One story in the Kingdom Come universe had Iris "Kid Flash" West encounter the Fiddler's great-grandson, Iowa Bowin, who believed his ancestor had "a headful of bad wiring", and wants to use his guitar version of Isaac's weaponised violin to be a hero.
The original Terra in Teen Titans turned out to be The Mole for the team and an unrepentant villain. Her first successor was a deliberate attempt to show a heroic version of Terra, to the point where some DC editors and writers even wanted her to be the original resurrected (this wound up averted in the end). The third Terra (who was originally planned to be an unrelated character) was even more of an example, as she lacked the second Terra's identity crisis issues and the original's sociopathy, and was a much more idealistic hero without much angst at all.
In Astro City, the heroine Quarrel is the daughter of a super-villain who was also named Quarrel.
There's an example of this in Watchmen where at the end of novel, Laurie discusses a change of costume design into one that looks like that of the Comedian, her father. While the Comedian was technically a hero, being the Token Evil Teammate of the original team of heroes, this example probably still fits.
In the Pony POV Series, Cadence in Dark World serves as this for Queen Chrysalis after defeating her and taking over the Changelings. From that point to her death, she turns the Changelings from vampiric parasites to symbiotic heroes who form a large part of the resistance against Discord.
Minuette is this to the Master, being a female regeneration of him using a fob watch. Once she learns of her true nature she fully rejects the Master's evil ways and ultimately feeds him to the Blank Wolf, erasing him from existence and sealing her status as a good guy.
Paladin of Have Gun — Will Travel is an interesting twist. Paladin was hired by a Cattle Baron to kill a gunslinger called Smoke, because he claimed Smoke was terrorizing a small town. As he lay dying, Smoke proved that he had been hired by the town to protect them from the cattle baron's thugs and called Paladin "Paladin" ironically. Paladin adopted the name "Paladin" and Smoke's all-black "working outfit", and set out to atone for his mistake.
Wataru, a.k.a. Kamen Rider Kiva is not this, despite there seemingly a tie between him and the Fangire King. However, his half-brother Taiga (full-blooded son of the King) definitely qualifies; not only is he more qualified for the throne, Taiga would later adopt his father's alter-ego, Dark Kiva, for the finale, just in time to work together with Wataru to battle the ressurected King. The series ends with the brothers in good terms, working together to create a peaceful co-existence between Fangire and humans.
Hunter: The Vigil: The life tenet of the Lucifuge is basically "we areSatan's children, but we protect humanity from the darkness". They are also the nicest Hunters when it comes to dealing with the more decent supernaturals. The other children of Satan, however...
To lesser extent, the Loyalists of Thule.
Exalted: Some of the modern Solars try to be this. Even the Abyssals and Infernals can at least try.
Amongst the canonical Exalted, the best example would be Swan, who is the Nice Guy of the iconic Solar circle. The previous incarnation of his Exaltation, a fellow by the name of Desus, was not.
Mass Effect 2 has Legion, a geth platform. While Commander Shepard has blasted through enough of these things to melt them down and rebuild the Normandy, Legion is a member of the true geth, which regards the geth Commander Shepard is familiar with as "heretics". These geth just want to be left alone, rather than leaving geth space and attacking.
In the Global Guardians PBEM Universe, the current Stuntman (a hero) is the only son of the original Stuntman (a villain). The father of Dream Catcher, a psychic hero with the power to turn dreams into reality, was active as a villain in the late 1970s/early 1980s and used the same name and the same powers (he's now in a mental institution).
Hot Wheels Battle Force 5: The Red-Sentients are the more war like race of Sentients (having been frozen to stop the war), and Krytus, their leader, becomes the Big Bad in season 2. When they are unfrozen, they exile Krytus as they are sick of war, and two new Red Sentients become part of the ruling council Korosivash and Karmakaris. While the former is kind and wants to help the people, the latter is arrogant, and looks down on his blue counter parts. However in the final act, he personally leads a brigade in to stop the Antagonists, and launches the hero out to beat the new Big Bad, cementing his own position as a good-guy, and as the new ruler of the council, washing away the treachery and evil Krytus brought to their species.
The Venture Bros.: In the show's backstory, SPHINX was a COBRA parody and terrorist organization that was wiped out by the OSI. In the show proper, SPHINX gets revived as a peacekeeping organization by former OSI agents disillusioned with the current leadership.
The Legend of Korra: The Fire Sages are peaceful, and they immediately try to get Korra help when they find her. Their Shaman setting her down in a spiritual place so she may recover from whatever has harmed her. This contrasts the original series where the Sages were completely loyal to the Fire Nation and stood against the Aang and the protagonists, bar their youngest member Shyu.