The Ultra Series fanfic Ultraman Moedari... well, you'd better see the paragraph yourself:
Meanwhile, Yapool fired a fireball. It bounced off. He fired more, but the behemoth turned and reflected them back. Yapool staggered as the now-enraged creature flung a bolt of light. Thousands of sharp spikes materialized out of nowhere, running him through while at the same time a small star surrounded him, while molted rocks bombarded him and crystals burst out of him. Twin daggers of some unheard of metal ran him through and through.
All this took place in a matter of seconds. The others looked on in horror: there was no trace of the powerful being.
Even worse when you consider his companions were cut to shreds in an instant by living, growing, creeping, PLANTS and Groza was reduced to a puddle despite being immortal.
One of Lunaram's Regina Finishers is kicking her enemy in the face... with an entire moon. The other is a blast of light as hot as the exterior of the sun. These destroy planets.
“What is it?” Torian replied, watching Tiger with a worried expression. Not too worried though, since her flaming crown had disappeared the moment she had doubled over in pain.
“The enemy temple! It's on fire!” the voice shouted.
“Huh?” He involuntarily looked down, and then kept looking, his eyes growing wider and wider. Something underneath the waves was burning bright enough to make them shine like the setting sun. “I- I can see that.” He looked up at Tiger, his expression begging for an explanation. “What are they burning?”
“Yes, you already told me that!”
“You don't understand! The stone is on fire! Underwater!”
Torian blinked. So did most of the youma.
“By all the dark gods, it just crashed and now the sand is burning too! Look at it!” another warlock shouted in the background.
“I think even the water is on fire,” the first one muttered in a voice that bordered on religious rapture.
“Don't be silly,” Tiger interrupted. “The water is too busy exploding to be on fire!”
“I... I stand corrected.”
That is all.
Mister Cynical's Lycanthrope series on fanfiction.net (loosely based on Neon Genesis Evangelion) is notorious for this, to the point where the characters in the series actually come to expect it. One notable example is where Shinji is supposed to kill a member of Seele in Paris. Instead of simply shooting him, he decides to blow up the building he's in, along with many others (including the Eiffel Tower). The end result is that Paris is filled with flaming debris which just happens to form a giant smiley face a mile and a half wide.
Shinji: Now those Frenchies have a smile they can be proud of!
Also, Finishing The Fight (found on the Halo Fanfic Recs page), in which much care is taken to describe the effects when "modern" UNSC weaponry is used on Dungeons & Dragons baddies..
Garrus. Need to question some criminals? Knock down the wall of their warehouse with a cargo hauler and shoot them all in the knees. Turns out they're not the ones who have what he needs to know? Knock down the next warehouse's wall with a cargo hauler and kneecap the men inside. Need to question a mercenary boss? Blow up his car with a tank.
Apparently, Admiral Nick "Havoc" Parker is known for this - according to Shepard, orbital bombardment is his first resort. The prospect of him and Garrus being in the same room is terrifying.
XCOM: Second Contact has X-COM's battle with the Turian patrol at Relay 314. The Turians have one cruiser and five frigates. X-COM brings 400 fighters, 12 cruisers, and 2 dreadnoughts.
In a crossover RPG (Fanon or Canon), Ancient Equivalents have invaded a faction on the level of the Ori (Tech, not power), and they have A LOT of drones (SG Fans Look Them Up), the defending forces just fired 'Vortex Beams' (Derived From Vortex Generation off of B5 Jumpgates) from the their ships, there were to many vortexes (700) that went critical resulting in the loss of a planet, two moons, 125 Ancient ships and 700 defensive forces. The vortexes merged and created a anomaly about 3 LS across :( Let's just say the person controlling the Ancients is not happy that they lost 1/3 or their fleet in the blink of an eye. The defending faction has something called a Planetary Defensive Grid well, you figure it out...
From Gods Of This New World: "Meanwhile, L had been in a harrier jet overhead… He readied a missile to be fired, and unleashed fiery hell on Mello."
In chapter 15 of Ace Combat: The Equestrian War, Flare Star reported (having witnessed it firsthand) that Blueberry was beaten to semi consciousness by four griffins before one of them ripped the wings off her body... Even after she hit the ground, her killer still smashed her spine to make sure she won't get up again.
From Strawhat Theater 2: Our Mrs Monkey: Absalom kidnaps and tries to forcibly marry Nami who's married to Luffy. Luffy uses Gear Second to punch him through several walls. And when Absalom turns invisible, Luffy uses Gear Third to punch the entire room through the rest of the castle.
The Witty Phantom's plan to defeat Stan in their rematch in Yu-Gi-Oh! The Thousand Year Door Redux is basically this. He summons Dice Reaper and uses his own Deckamster ability to make it unkillable by card effects. He then uses the Dice Reaper's effect to rig his dice rolls by basically getting to choose what number he would roll instead of actually rolling dice. By using Take a Chance's effect to multiply his life points by five by rolling a six, the Phantom's life points go from 6,500 to 795,000. But the overkill part is the Phantom summoning Ancient Sacred Wyvern, who gains Attack Points equal to the difference in Life Points if its controller has more than his opponent, resulting in a monster with 780,500 Attack. It fails due to Stan's facedown, Magic Cylinder.
In The Jaded Eyes Series when it's Harry's turn to fight the orcs during the Triwizard Tournament. The task is just to "use any means to retrieve the gold pieces" and Harry does just that... by slaughtering them all and picking their corpses.
The Albacore crew in The Nowakverse has the so-called Darned Nearly Recoilless Rifle. .22 rimfire ammo doesn't sound like overkill until you realize that the Recoilless is used by small rodents for whom .22 is about as large as a 155mm howitzer is for humans. It is shoulder-fired, and it requires a second rodent to reload it from behind. Nevertheless, the Recoilless is used as an anti-personnel weapon.
XSGCOM has this as the X-COM's SOP. Their reaction to most things is to nuke it, or if it's not enough then nuke it with bigger nukes. And if that's not enough, ask Tollans for even bigger ones.
In the Stargate SG-1 fanfic Far Beyond Normal, Lt. Colonel Fenton of SG-13 uses "over a hundred people" of whom "even the ambulance drivers and helicopter pilots were Special Forces trained" to capture an unarmed 18-year old human girl loose in Colorado Springs. He reflects that "One of the things he loved about the SGC was that nobody minded if it took a sledge hammer to drive home a nail, so long as the sumbitch got drove." The girl in question turns out to be Buffy Summers, so in hindsight it was just-barely-enough-kill.
In Mega Man Recut, Wily decides the best way to deal with a shrunken Mega Man is a submachine gun.
In Mega Man Reawakened, Robert at one point uses a Program Advance to destroy a breakable wall. There's nothing left of it when he finishes.
In The Art of the Deal, Naruto deals with Yakuza using his warehouses to smuggle drugs by hiring the Akatsuki with orders to "leave a lasting impression". According to Kakuzu, for the amount they're being paid, he can demand anything he wants.
If it involves X-Com, this is there standard operations, with levels of overkill ranging from planet burning to enough to cause a pre-emptive surrender in anybody but those with the idiot ball firmly in two hands... Those two hands tend to become vapourised, along with anyone related to the person whos hands they were within a fairly large radius.
The Infinite Loops has "Seapony Diplomacy". Their solution to an infestation of Xenomorphs? Once they discover that the xenos aren't friendly, they glass the planet. Then they blow up the planet. Then they throw the remains of the planet into the nearest sun. Then they blow up the sun. All while merrily singing and laughing. This is their usual reaction to most problems: throw explosives at it until the problem is dealt with.
Wings To Fly: Gundams do not die easily, and people know this. This results in such situations as five Gundams being targeted by 288 missiles, and a squadron of Super Leos volley-firing their 203mm shoulder cannons into one, smashing it with nearly 30 rounds of 8" shell that blow both its cockpit and reactor out its back in shreds. Once in close combat the kills actually scale down in violence because there's not enough time to be so violently thorough.
Mirrors Image: Pinkie finds that someone has broken, stomped on and burnt the Pony Polka record she had ready for Cadence's wedding, leading her to suspect somepony may not like it. It was Princess Luna. Luckily, Pinkie has a copy.
When Naruto wants to make sure an Akatsuki base is destroyed, he turns everything in a 1.2 km radius into molten slag. To be fair, he had been force fed the jutsu by the Nine-Tails and did not now how powerful it was.
When Hinata kills Madara, to make sure he is absolutely dead, she atomizes him with a black hole/Rasengan hybrid.