Housepets! has Fox doing this to King, after he turn back into a human, Joel.
Prequel is, 90% of the time, hilarious takes on the Elder Scrolls world. Another 9% is watching the main character, Katia, fail rather spectacularly at everything she tries. The last 1% was a dream she had, wherein a monstrous king/spider/dragon appears, impales her best friend through the chest, then hunts her through her own dreamscape as she desperately drags herself away. When she finally rises to face him, he pins her abdomen to the wall.
Siegfried from Dominic Deegan has a bad habit of inflicting these on others when he loses his temper. Dominic's been on the receiving end of such a beating twice. Now that he's become a demon, Siegfried has eschewed physical beatings in favor of Mind Rape and Demonic Possession.
From Homestuck, In response to Vriska having murdered her previously,Aradia attacks her at the end of [S]: Make Her Pay and delivers the most merciless beating we've seen in the comic so far, leaving Vriska unconscious on the ground and covered in her own blood.
Also, when Jake meets the young Troll Empress (alias "sea Hitler"), he fails to hear his friend telling him that she's an alternate timeline version of her, not to mention already dead. He decides to kill her before she grows up, pounces on her and attempts to punchnote either he forgot he had guns, or they didn't "follow" him to that Dream Land her to death. He doesn't stop until another character knocks him out.
When the characters fight on LOFAF, Terezi attacks Gamzee with her canes, giving him a "Reason You Suck" Speech about how he treated her. She shouts at him to fight her, but Gamzee, being mind-controlled, doesn't bother defending himself, and smiles vacantly while she cuts into him. When the control is broken, he flips out and pummels her quite severely, it's even lampshaded when Rose shouts at him to stop and tries to intervene.
John, after being teleported to Caliborn by his plot powers, realizes that Caliborn is Lord English and therefore responsible for the murder of billions. John's beatdown is only stopped when his plot powers randomly teleport him away.
And in these twostrips, Xykon utterly thrashes Spliced V. It starts with trap glyphs, Energy Drain, Maximized Energy Drain, another Meteor Swarm, and Superb Dispelling. Xykon finally ends it by hitting V with a chunk of the wall hard enough to cause V to lose his/her grip on the spliced souls. Then, he stops holding back, ending with him shoving his hands down V and O-Chul's throats, ready to Meteor Swarm their heads apart.
And don't forget the climactic fight of Start of Darkness.
Even Xykon himself is not immune from this, as seen when the ghost of Soon Kim pounded both him and Redcloak, and would have succeeded in killing them both were it not for Miko.
In Shape Quest, Tonya (who is not a villain) finished off Lance in the Scarlet City tournament without him giving her too much of a scratch.
In the end of chapter one (and only) of Jesus Christ: In the name of the gun the title character took two pages to liquefy (sic) Hitler's (who happens to be a werewolf) skull. With a cross-shaped gravestone. Starting here.
Imperial Lieutenant Janek "Tank" Sunber, one of Luke Skywalker's childhood friends, has just helped capture a rebel base when he walks into an interrogation room to find two junior officers beating the hell out of a rebel prisoner. He immediately tells them off, only to hear the prisoner taunt him with Luke's destruction of the Death Star — with Luke's "betrayal" of the Empire and Tank. The other officers grin as Tank joins in the beating — then suddenly their grins are replaced by frowns, then looks of shock as they pull him off of the man to stop him from killing him with his bare hands.
Achewood has the Great Outdoor Fight arc... which ends with a No-Holds-Barred Beatdown of the event venue itself. (The term "full service beating" is used as well.)