Technarchy and Phalanx members (Marvel Comics); via "techno-organic virus"
Phoenix Force and her avatars (Marvel Comics)
Living Tribunal (Marvel Comics); pre-retcon
Dr. Solar (Valiant Comics)
Species 8472 (Star Trek: Voyager)
Many alien civilizations and powerful characters (Doctor Who)
Captain Planet (Captain Planet and the Planeteers)
Various Characters (Dragon Ball series)
The Phoenix (Fairy Tail: The Phoenix Priestess); via the process of rebirth
Sailor Saturn (Sailor Moon)
Sailor Galaxia (Sailor Moon)
Boros (One-Punch Man)
Angol Mois (Sgt Frog)
Ikaros (Sora no Otoshimono); via the Hephaestus Cannon
Lucy (Elfen Lied)
Seraphs (Bastard!!); Stated, but not shown
Quat Nevas (Pysren)
Hellstar Remina (Hellstar Remina)
Bellcross (Heroic Age)
Asura (Asura's Wrath)
Chakravartin (Asura's Wrath)
The Destroyer (Legend of Spyro)
Dark Gaia (Sonic Unleashed)
Sephiroth (Compilation of Final Fantasy VII)
Vegnagun (Final Fantasy X-2)
Bhunivelze (Final Fantasy)
Planet Buster (Spore)
Grey Goo (Tasty Planet)
Collapse (Valkyrie Crusade)
Demise (The Legend of Zelda: Skyward Sword)
Herman the Planet Smasher (Devin Townsend Project)
Black Star Dragon Balls (Dragon Ball GT)
Planetary Annihilator (Futurama)
Illudium Q-36 Explosive Space Modulator (Looney Tunes: Rabbits Run)
Eclipse Cannon (Sonic the Hedgehog)
The Death Star (Star Wars)
Starkiller Base (Star Wars)
Conquest Ray(Ben 10: Alien Force)
Planetomic missiles (Fireball XL5)
Shi'Ar Empire Nega Bombs (Marvel Comics)
Anihilation Wave "Harvester of Sorrow" (Marvel Comics)
Asgardian Destroyer Armor (Marvel Comics)
Mister Knife Flying Fortress via missiles (Marvel Comics)
The Cluster (Steven Universe)
Gourmet Cells (Toriko)
High-Tier Longinus (Highschool DxD); considered to be the biggest 'bug' in the Sacred Gear System made by God, are four of the strongest Sacred Gears with not just the potential to kill other Gods, but are also capable of destroying the world.
Herman the Planet-Smasher (Devin Townsend Project) is a creature who's voice could destroy planets, galaxies and everything else in the path of its voice
Vegeta (Dragon Ball) using the heavily charged Galick Gun, with the intent to destroy planet Earth.
Goku (Dragon Ball) as a Super Saiyan, has a kili level of 3,000. It was stated that at 200-300 kili, one could destroy 1-2 planets.
Frieza (Dragon Ball) uses the Earth Breaker attack...
...to detonate the Earth.
Like his younger brother, Cooler's (Dragon Ball) Supernova is powerful variation of the Death Ball. As such, it is capable destroying entire planets, reducing them and everything on them into dust.
Broly's (Dragon Ball) Omega Blaster is his most powerful attack, capable of destroying an entire planet with ease.
Cell (Dragon Ball) firing the aptly-named Earth-Destroying Kamehameha.
Cell (Dragon Ball) states that his Solar Kamehameha can destroy not just the Earth, but the entire solar system.
As described by Goku, Kid Buu's (Dragon Ball) Planet Burst has enough power to destroy the Earth ten times over.
Omega Shenron (Dragon Ball) using the Minus Energy Power Ball with the intent to destroy Earth.
Beerus, the God of Destruction (Dragon Ball) destroys planets to maintain universal balance.
Dark Gaia (Sonic Unleashed) exists solely to destroy the Earth every few thousands of years in a cycle of destruction and rebirth.
Bender Bending Rodríguez (Futurama) wielding the Planetary Annihilator, which fires a deadly beam capable of living up to the weapon's name.
Kurohime (Magic User Kurohime) wielding the Ultimate Sword that can cut through even an entire planet.
Sailor Saturn (Sailor Moon) can destroy entire planets using the Silence Glaive.
Collapse (Valkyrie Crusade) destroying a world with her fingers.
After being summoned and granting a wish, Ultimate Shenron (Dragon Ball GT) will cause the planet on which he was last summoned to explode unless the Black Star Dragon Balls are all collected and returned to said planet within one year.
Using his cosmic axe, Terrax (Marvel Comics) cleaves an entire planet in two.
The Destroyer (The Legend of Spyro) exists to bring about the birth of a new world by destroying the old one.
When powered by all seven Chaos Emeralds, the Eclipse Cannon (Sonic the Hedgehog) can destroy the Earth...
...though when powered by only six, it has enough power to destroy half of the moon.
Vegnagun (Final Fantasy X-2) is a machina weapon powerful enough to destroy all of Spira.