To be fair, Did you just RAPE Cthulhu is also an accomplishment. In the last Episode the UnravellerofMysteries, a literal God of Evil undressed and penetrated Ami. Ami wasn't really enthusiastic about it and after it was over the Unraveller told Ami to call her up again. But Ami doesn't think so, because really, she didn't feel a thing while it lasted and was only sore afterwards.
A mod over at Toho Kingdom writes yearly holiday themed fanfics with members of the site as character. Last Christmas fic featured Cthulhu as the main villain. After the military fails epically to kill him, they get a pair of mecha from Santa Claus and manage to kill him.
In Dumbledores Army and the Year of Darkness, Ernie Macmillan has the stones to punch out a Dementor. Yeah, he goes down... but he tried. And he gave his secret wife, Susan Bones Macmillan time to whip out her wand and summon her Patronus.
During his first appearence in the Tamers Forever Series Chaosgallantmon absolutely DESTROYS both Azulongmon and Zuqhaiomon in about ten seconds flat.
In Manchester Lost, Crowley punched Lucifer - In the FACE!!! There's also the part where War yells, "Mommy, you're an idiot!" followed by decapitation.
In My Immortal, it is the reader. This really isn't much of a surprise, giving its reputation, but screw it. I wanted to test the spoiler cover's powers.
The Spore wiki fiction universe has a rather epic one involving the hero fighting and actually defeating Satan(A.K.A. Kamik'Shi) and then sealing him in the sword that stabbed him.
The Mane Six's previous defeats of Nightmare Moon and Discord, of course, but they add two to the count with the defeat of Nightmare Whisper and Applejack teaming up with five alternate versions of herself to defeat Nightmare Mirror.
Pinkie and Minty managed to defeat Princess Luna with a musical number during the Cosmic Retcon of G3. Even though Strife had weakened her, that's still a great accomplishment.
The Paradise Estate Ponies, even taking into account they had three Alicorns supporting them (all three were considerably weaker than him), managed to defeat Discord in a straight up fight with the Rainbow Of Light. Unfortunately, Galaxia decided to shatter him, allowing him to Body Surf into a new body.
Dark World!Spike manages to get the upperhand on Rancor, the Draconequus of Violence, Passions, and Anger, and force her into retreat temporarily. She is a young Draconequus, but still.
The Dark World Mane Six managing to defeat Odyne!Cruelty, first destroying her body (unfortunately killing the possessed Sparkler in the process), then by blasting her soul with the Elements, banishing her from mortal reality.
In the one-year anniversary chapter of You Got HaruhiRolled!, the author wreaks havoc by summoning a giant, animate cheesecake which goes about destroying everything it comes across. The author spends so much time gloating that he is unstoppable that he doesn't notice the main characters travel through his portal to another of his fanfictions. The fic they travel to is The Obesity of Haruhi Suzumiya, an Alternate Universe fic in which every character is morbidly obese. They take this fic's version of Haruhi with them, and she devours the cake in a matter of seconds. Not to be outdone with that, Kyon defeats the author by informing him of the existence of a truly NSFWDoujinshi. note Which actually exists, but I would advise against looking for it. The author's disgust makes him sink into a literal Plot Hole, and Haruhi sits on him.
Harmony Theory: Rainbow, Astrid and Star Fall acttually manage to chase off Nightmre Umbra. However, Umbra is still regaining her strength.
Death Note Equestria: When Applejack is exposed as the Third Kira, she hits Princess Luna hard enough to send her stumbling back.
The Conversion Bureau Cold War: When Princess Xenole... I mean, Celestia repeated threatens a UN conference full of world leaders, and kidnaps and tries to justify the forced conversion of over 2,000 Chinese civilians, Ronald Reagan finally has enough of her shit and punches her right in the face.