The Seven Deadly Sinsbeat Death to death as well. Considering that the Sins aren’t as powerful as you might think, this makes it more epic. Or would, if a certain Virtue didn't come in and make the finishing blow.
Gunnerkrigg Court: Kat punched the psychopomp Muut in the gut beautifully sculpted abs after finding out what Muut and the psychopomps had done to tick off her best friend Annie. It didn't do anything to Muut, but more importantly nothing happened to Kat, who basically attacked (a) Death with her bare hands. As the author said, "Do you have a friend that would do the same for you?" A link for your amusement.
The Headmaster: Do you realize how many people could slap a creature like Coyote on the rump and live to tell about it?
And Jack forcefully tearing Reynardine from his assumed body.
In 8-Bit Theater, Red Mage cut open the head of a being capable of boiling the atmosphere. They would have achieved this again towards the end, but Sarda was beefed up from the orbs and had his power further amplified by Black Mage's super evil.
Chapter 10, "K'Z'K": Riff and Torg have just released the über-demon K'Z'K who is supposed to end the world. Then they hit him with the time blaster, freezing him in place. (But then he gets sent back in time to conquer the past.)
"The Storm Breaker Saga": K'Z'K is about to squash Torg and Zoë personally to keep them from preventing him from conquering the past, and swipes away the Book of Güd that they were about to use against him from Zoë's hands when she says she can't read it. The power of the pictures in the book reduces him into a bug-like creature, and Zoë steps on him.
"That Which Redeems": The Talking Weapon Chaz, which when powered with the blood of the innocent can kill pretty much anything, suggests that Torg use it to destroy the DemonKing. He doesn't actually follow on this plan, but during their escape, the Demon King intercepts them and strikes down at them with a sword formed out of his own darkness. Torg parries with Chaz, and just that is enough to throw the Demon King off and scar him.
One Two Lumps story arc featured a Cthuloid being that disguised itself as a mop to get into the house. Eben dealt with it in traditional feline fashion.
Homestuck: The Black King of the Troll's session also counts. Twelve prototypings, one of which was an Eldritch Abomination, made it monstrously powerful, but they all still managed to lay the smack down and beat the game. And makes the denial of their ultimate prize for beating it all the more tragic.
In [S] Wake, Aradia, albeit temporarily, manages to timestop Bec Noir.
Jack Noir, wearer of the ring of the Black Queen, powerful enough to slaughter two armies by gesturing and armed to the teeth with prototyping powers has his ass handed to him not once but twice by Bro Strider, Lil Cal and eventually Davesprite- a kernelsprite that isn't supposed to take out enemies above level 2, a guy who films ironic puppet porn and one of his most popular ventriloquist acts.
In Mortifer, it was "Did you just shoot Lucifer in the face?" Of course, it only stuns him... Which is why Joey went to the precaution of having his gfirlfriend kidnapped. When we cut back to them a chapter later, Joey walks out of the room covered in blood, and asks his henchmen to deal with the body. Also, a flashback reveals that the reason that Joey became one of the fallen was because he killed a god and, it's implied, several angels as well. It seems that he's making a habit of doing this... Which is ''not'' a good thing.
In an issue of The Word Weary, Jason comes face-to-face with the Goddess Queen of the Sun while passed out drunk and opens a bottle of beer on her teeth. The trope is played with in that the sun goddess, while strange and hideous, seems kind and compassionate.