In Code Geass, Suzaku almost constantly, because he has an enormous Guilt Complex. Lelouch also later on, as he does more and more morally dubious things for his cause.
In Monster, when Grimmer calls him a doctor, Tenma goes on an angsty tirade about how he is not worth the title because he killed someone. He doesn't know at the time that the person he thought he killed is still very much alive.
Eva also goes through a period of this when she realizes how badly she has been treating Martin (and how much worse she had been to Tenma).
Beelzemon from Digimon Tamers initially refuses to do a Heel-Face Turn, not because he doesn't want to, but because he sold his soul for power, went on a murderous rampage, and killed one of the heroes. Even after the Tamers forgive him and reassure him that he's one of them, he never, ever forgets what he did.
In Realm of Kings: Son of Hulk, Arcturus Rann of the Micronauts reveals that he visited Jarella's homeworld K'ai more than a thousand years ago and in a moment of extreme prejudice, massacred most of the civilization due to a perceived threat to Homeworld. This also creates a big Plot Hole and Continuity Snarl since Rann's Microverse originally existed in a separate one from Jarella's. It wasn't till recently that they merged, postdating Rann's visit by 1,000 years.
In the Pony POV SeriesFluttershy actually ended up doing a lot of good as Princess Gaia/Nightmare Whisper, despite all the bad she also did. When given a celebration for the good she did (and that she was able to have the self control to at least TRY to do good when given the power of a goddess), she outright says there's a lot of things she did she'll never forgive herself for and she doesn't blame the ponies who won't forgive her for what she's done. She accepts those that will, but she'll never forget what she's done.
Kado from Tokyo Demons faces tremendous guilt for everything he's done, including becoming a tool for Touya. Half his dialogue includes apologies. Whether or not it's justified guilt is another matter.
The novel All My Sins Remembered by Joe Haldeman. The hero is a spy/operative for the galactic government. The novel is a series of debriefings where he tells what he had to do in the line of duty, and how those memories are gnawing on his conscience. The true horror of it is that in each case, his actions should have served to make the universe a better place, but his sacrifices were screwed over in the name of Realpolitik, and his "debriefings" are in fact part of memory-erasure "therapy" that are reducing him to a drooling vegetable.
The Book Ends to Luke Skywalker and the Shadows of Mindor, which take place after the story that elapses between them, make Luke into this. He actually hires an investigator to look over events and build a case against him. The investigator writes a holothriller script instead.
In It Can't Happen Here, Doremus blames his own passivity (and that of others like him) for the ascendancy of totalitarianism in America. He expresses this sentiment in a scathing column criticizing Windrip:
"The tyranny of this dictatorship isn't primarily the fault of Big Business, nor of the demagogues who do their dirty work. It's the fault of Doremus Jessop! Of all the contentious, respectable, lazy-minded Doremus Jessops who have let the demagogues wriggle in, without fierce enough protest ... I can blame no Aras Dilley, no Shad Ledue, no Buzz Windrip, but only my own timid soul and drowsy mind. Forgive, O Lord!"
Being Human: Mitchell actually wants his sins forgotten, because for the vampires they're a source of inspiration. Still, the spirit remains - he doesn't want acclaim and admiration when he's primarily focusing on his all-consuming guilt.
Londo Mollari toward the end of the series. In fact, in the twilight hours of his life, he tells two children and their nurse his pivotal but silent role in the Earth-Mimbari War and the actions he committed which had stopped a major chance for peace between the races.
Along the same trajectory as his sworn rival, G'kar's transformation from conniving diplomat to the major religious figure of his race by the end of the series. So much so that he exiles himself to deep space to get away from the unwanted adulation of his followers.
Brother Edward, a monk who discovers he was a serial killer before his death of personality. He ends up resigning himself to his death at the hands of his victims' angry relatives in contrition..
Again, inverted in Mark Antony's speech over Caesar's body, in the play Julius Caesar. Antony says he is not there to praise Caesar, but clearly that is exactly his intent, as he recounts the evil (but charitable and heroic) deeds of Caesar.
Joshua Graham of Fallout: New Vegas has this mentality in the Honest Hearts DLC. When you're the co-founder of Caesar's Legion and responsible for atrocities such as rape, slavery, torture amongst other things, you honestly do have a lot to answer for.
In Final Fantasy Tactics, Delita Hyral ends up murdering or manipulating almost everyone he ever knew, to become king. The final scene of the game involves him lamenting over Ovelia, his dead wife and queen, wondering if it was all worth it.
Solid Snake from Metal Gear Solid. He doesn't like to be called a hero. He feels he's just a killer. Summed up in this line from MGS4
"I'm no hero. Never was. Never will be. I'm just an old killer, hired to do some wetwork."
Dinobot, the Heel-Face TurnBlood Knight of Beast Wars, says something like this on his death bed, following a Heroic Sacrifice where he saves the human race, despite the fact that their annihilation would guarantee his ancestors win the great war. He knows he's done some questionable things and has to answer for them. He tells his Maximal comrades that he should not be regarded as a hero, but that history should judge him.
And it has. Dinobot is regarded as one of the greatest characters in the entire Transformers franchise.