Preacher: Ah, Herr Starr, where do we start? Let's see, when he's introduced, he's already blind in one eye with a nasty scar around it, but as the series goes on, he gets anally raped by a perverted sexual investigator, his left ear shot off, his bald head has a line cut into it that makes it resemble a penis, he loses a leg to a pack of cannibals, and finally has his penis and testicles bitten off by an angry attack dog.
Bone: Kingdok goes through a gradual, but nonetheless brutal one as the series progresses. First, he gets his arm cut off by a girl just learning the ways of combat. Then, he gets his tongue ripped out by a giant cat. Later, he is buried alive after an earthquake, though he survives by falling into a series of underground caverns. His superiors decide to use him as a last line of defense for the local Cosmic Keystone. So they put him under mind control and force him to march through the caverns for days on end before he finally reaches the keystone. By then, the once proud warrior king is so broken and humiliated that he deliberately invokes You Killed My Father on one of the protagonists in the hopes that she will kill him. (He had killed her parents well before any of this, he just decided to bring it up then.)
In the third issue of Marvel's Siege event, Norman Osborn, one of the Marvel Universe's most dangerous supervillains, who has basically been in charge of U.S. homeland security for a year, gets put through one hell of a conga. First Captain America, the living embodiment of all the principles Norman's betrayed, announces his resurrection by hitting Osborn square in the face with his shield, and then beating him in a one-on-one fight. The president of the United States orders him arrested for treason and has his flying base shot down. Iron Man, whose technology Norman stole to turn himself into the "Iron Patriot," comes back from brain death to shut down Osborn's armor. When the costume falls off, Norman is revealed - on national television - wearing clownish facepaint modeled on his old "Green Goblin" identity. And finally, as he rants about how the fight isn't over, Spider-Man, his oldest enemy, says "Oh, will you shut up?" and decks him.
Daredevil: In Born Again, Daredevil's secret identity is sold to the Kingpin, who makes his life living hell. Matt loses his job, gets his credit cards canceled, gets accused of criminal misconduct, gets stabbed and almost killed, and becomes homeless, among other things. He finally turns the tables and manages to start ruining Kingpin's life by revealing that Kingpin sent a madman to destroy Hell's Kitchen.
Matt Fraction's approach to writing Iron Man appears to come down to turning his life into this. Tony Stark loses his company, his fortune, his memories, his life, his brilliance, his dignity, his girl, his sobriety and even his legacy in the distant future. It almost seems too much to not be intentional.
Garth Ennis penned a two-part story early on in his run on The Punisher where guest star Wolverine gets some particularly brutal treatment. Just one quarter into the story he gets his entire face blown off by the Punisher's shotgun (and spends the rest of it with his adamantium skull showing), he's clubbed and later shot in the crotch, gets a chainsaw taken to his ankles (though manages to kill the guy before they're entirely cut) and then gets crushed by a steam roller at the end of the story. Although Ennis, who's known for having a dislike of costumed superheroes (Superman aside) notably handled previous guest-stars like Daredevil and Spider-Man pretty roughly, what he did to Logan seems particularly overboard.
The debut of Red Hulk was heavily critiqued because it seemed to turn him into a Villain Sue - he beat up Iron Man, beat up Thor with Mjölnir (something that should have been impossible), and beat up Uatu the Watcher. So when Jeph Loeb left the book and Jeff Parker took over, the whole thing started with one big karma tour. Iron Man trounces him when they have to team up, Thor weighs his hands down with Mjolnir and dares him to try and lift it (he can't), and when he's stranded on an asteroid headed towards a black hole, Uatu shows up and says he could interfere, but won't... "For I am merely THE WATCHER."
Rastapopulous in Flight 714. He first appears looking ridiculous in a cowboy suit with pink shirt and shows himself unable to crush a spider. Next he is accidentally injected with a truth serum and starts arguing with Laszlo Carriedas over who's badder. He is then Bound and Gagged by the heroes, has a thorn prick him in the rear, and though escaping is hit on the head with a broken rifle. Then he runs into a tree and has the tape painfully ripped off his face. After that he gets caught in the explosion of a grenade, accidentally elbowed in the face by Allan, and when he finds the bump on his head has gone and takes that as an omen his luck is changing an earthquake causes a stalactite to fall onto his head.