The ending of Green Legend Ran anime results in this. For decades the Earth had been reduced to a wasteland due to an alien influence, and when the Big Bad was finally defeated, Ran and his Magical Girlfriend magically restored the Earth back to what it used to be.
At the end of RahXephon, it is revealed that the instrumentalist can create a world according to their will. Ayato's choice creates a world where all the people he loves are happy, and the Mullian war never happened.
The ending of the first season of Sailor Moon. It's also implied that Crystal Tokyo is herald in when Neo Queen Serenity ascends and pulls one of these for the entire planet after some global freeze/disaster.
The plot of almost every Dragon Ball story arc inevitably involves using the Dragon Balls to generate one of these. To the point where in later episodes, they hardly even worry about the damage they do fighting the Big Bad because they know they can do this once they're done defeating the Big Bad.
Yukio Oikawa does one at the end of Digimon Adventure 02 by using the power of a world were dreams come true to convert himself into energy and revitalize the Digital World. Justifed at least in this case because, as the way he did it was previously explained.
In Digimon Frontier, the world was in disarray because bad guys had stolen important data. We sometimes got to see ruined areas restored after the fall of the Monster of the Week early on. In the final episode, the entire Digital World had been fed to the Sealed Evil in a Can to fuel his full restoration, and he plans to make a new world in his image. When he's taken down for good, we get to see an entire world — the Digital World in its natural state, seen only in flashbacks until now — form from shiny barcodey lights.
At the end of Kanon, Ayu's miracle undoes all the tragic deaths occurring earlier in the series and heals Akiko.
In CLANNAD, there's a smaller version of this. The Girl from the Illusionary World manages to use the Orbs of Light brought by Tomoya (as the Garbage Doll) to cause a Retcon; it saves Nagisa from her Death by Childbirth and Ushio from her illness, while also healing Fuuko from her coma.
In Puella Magi Madoka Magica, this is, more or less, the result of Madoka's wish in the final episode. Magical girls and others who are killed by witches get brought back. Magical girls who became witches, on the other hand, are whisked away to Magical Girl Valhalla by Madoka at the moment when they would have become witches. Madoka herself is removed from existence because she would have become an even more powerful version of Kriemhild Gretchen otherwise.
In D.Gray-Man, having the Musician play the piano in Noah's Ark reversed the download which restored the setting as well as all the characters who hadn't been killed in battle.
Massively subverted in Tenkuu Senki Shurato. The Goddess Vishnu releases one when she's restored to normal after having been Taken for Granite, repairing the Tenkuukai and reviving her fallen Hachibushu warriors. However, it has two drawbacks: she cannot revive Gai due to external influences... and when the one who intervened appears (Shiva, Goddess of Destruction), the Tenkuukai starts falling apart again.
With Strings Attached: When the Hunter stabs the Heart of Evil on the Plains of Death, it releases a massive, ball-shaped burst of energy that spreads out over the Plains, destroying all the undead massed there and triggering rain in clouds that had been sitting there for ten years. Later, Ringo notes that some old seeds in the ground have started to sprout.
Fallout: Equestria has The Gardens of Equestria. Twilight Sparkle's greatest creation, a megaspell powered by the Elements of Harmony able to cleanse all Equestria of all the radiation and taint created by the end of the war and return its ability to be a paradise again.
Played with in Ace Combat The Equestrian War. The Mane Cast use the Elements of Harmony powered up by Celestia and Luna's magic to slowly rejuvenate Equestria to the state before the war with the griffins. However, all characters that died during the war stay dead.
The use of six sets of Elements of Harmony to defeat Nightmare Eclipse once and for all lets off a timeline healing wave that breaks the "Groundhog Day" Loop she turned the Dark World timeline into and fixes the damage she caused to it.
At the climax of The Dashverse story Hot Heads, Cold Hearts, and Nerves of Steel, when the Elements of Harmony and the Crystal Heart are combined against Sombra, the released energy blast depowers him, cleanses the Crystal Empire of his taint, and seals his Windigo servants in a crystal cage.
Yellow Submarine. As the Beatles sing "All You Need Is Love", all of the things destroyed and people frozen by the Blue Meanie attack are restored to wholeness/life.
The Sprite from the "Firebird Suite" segment of Fantasia 2000 uses her Fertile Feet to restore the ashen landscape after the devastation brought on by the Firebird.
After the Beast transforms back into the prince in Beauty and the Beast, magical sparks spread across the castle and transform it back to its original state, with the gargoyles transforming into angels and the darkened walls turning to alabaster.
The end of South Park: Bigger, Longer & Uncut has Satan use one of these to restore the world (or at least North America), including bringing everyone back to life. Except Kenny, who has to go back to being dead.
In the original TRON, when the MCP is destroyed, all of the red lines in the landscape turn to blue (indicating the end of the MCP's influence) and all of the I/O towers light up, showing that programs can communicate with their Users again.
At the end of The Neverending Story, when Bastian starts making wishes Fantasia is recreated the same as it was before the Nothing destroyed it.
At the end of The Dark Crystal, once the Crystal is healed, Kira is returned to life and/or her mortal wound is healed, the podling slaves regain their life essence, and the blighted landscape around the Crystal Castle is restored to Edenic glory.
At the end of The Matrix: Revolutions, the entire Matrix is returned to normal using a cool sci-fi effect and the requisite black cat.
The earthquake resulting from the restoration of the Earth's core to its normal spinning state in The Core is described by DJ Qualls's character as "one giant shock wave" in which "the Earth is healing itself!"
Sgt. Pepper's Lonely Hearts Club Band. The wave of goodness that passed over the town of Heartland at the end of the movie, canceling out all of the effects of Mr. Mustard's corruption.
In Star Trek II: The Wrath of Khan, the Genesis Device is a World Healing Wave weapon. When fired at a planet, it converts the matter on the surface into life-sustaining matter, in effect terraforming the entire planet in days instead of years. It is shown to have worked on a cave, and in the end it is detonated in a nebula, building an entire planet from scratch. Star Trek III: The Search for Spock, however, shows that it doesn't actually work. Said planet goes through its entire lifecycle (from newly formed planet to catastrophic destruction) in what is implied to be a week or two at most. This because its lead creator, Captain Kirk's son David Marcus, used unstable protomatter in order to basically cheat his way into completing the thing, showing he's Not So Different from his father.
The trope is also subverted in that Genesis doesn't discriminate in what it converts. Whether dead rock or populated planet, everything on the surface is getting culled for Genesis to do its thing. This becomes a big issue in the next few movies, because Genesis represented one of the deadliest weapons known to civilization: a weapon that could not only kill all life on a planet, but leave a perfectly healthy biosphere behind for whoever did the killing (or at least do the first part when they discovered how unreliable the creation part was). Worse, it may actually work just fine. It was meant for use on dead planets, not what specks of matter it could pull together from a nebula. Apples and oranges, only more so. Though shortcuts were taken, (and for a casual fan, there's no knowing where the Expanded Universe stands on the matter) from what we got onscreen, a warning label on it that says "actual planet required" may be all that is necessary for the thing to go operational. It would be very bad if misused.
In the end of Good Omens, Adam makes it so that the world will not remember the day that just passed and all that happened is undone: the Book shop did not burn, the Bentley is new again and no-one died.
Semi-example at the end of the Mistborn trilogy, after Sazed ascends to godhood all the damage that the Lord Ruler and Ruin did to the world is fixed, the ashmounts get sealed up, and there are flowers. It's only a semi-example because he hadn't figured out how to bring dead people back to life, so most of the original population is dead, but at least the survivors are safe and get a fresh start in a much better environment.
A classic example from ""The Chronicles of Narnia: in The Lion, The Witch, and the Wardrobe'', when Aslanreturns, his presence alone is enough to end the hundred years of winter created by the White Witch, first bringing Christmas, then making flowers bloom and melting the frozen rivers without flooding. Within a day or so it has become early summer, restoring the natural balance. Characters that had been turned to stone by the Witch are revived by Aslan as well, though that takes more direct intervention.
Averted in the book Kingdom Come, as God and Jesus spend a few months restoring the earth to its former beauty following the end of the Tribulation to make it new for the Millennial Kingdom.
Also possibly played straight in Glorious Appearing, when a nearly devastated Jerusalem is instantly restored and void of any dead bodies littering the streets after Jesus gets rid of the Global Community.
The Great UnDoing in Septimus Heap works like this, and recovering its text is a major plot point in Darke.
At the end of the final book in Gael Baudino's Dragon Sword trilogy, the first act of Alouzon after her apotheosis is to heal the land of the ravages of unleashing the equivalent of the Vietnam War-era United States Armed Forces on it.
The Dakara Super weapon in Stargate SG-1 was originally designed to do this. Of course, given that it's called a "weapon"... It's more a tool that can be used as a weapon. It unleashes one of these to demolish all the Replicators in the galaxy in "Reckoning, Part 2". Of course, it's a World-Wrecking Wave if you happen to be a Replicator.
The wave of goodness caused by Zordon's death at the end of Power Rangers in Space which either killed or turned good all the villains from that point to the beginning of the franchise.
Power Rangers Lost Galaxy end with the returned Sabers restores the people of Mirinoi. Even less understandably it revives the dead Pink Ranger (the character died because the actor was ill, and the actor had recovered by the time of the finale).
Emma's good-bye kiss to Henry in the season ender of Once Upon a Time not only brings the kid back to life, but breaks the curse on the entire town of Storybrooke. Of course, so sooner had it happened than Rumplestitskin decided to trigger a spell which might invert the trope.
In Nightwish's song Devil and the Deep Dark Ocean, once the Devil is defeated, the angels declare that "We shall come to set the dolphins free/We shall wash the darkened bloodred sea/Our songs will echo over the mountains and seas/Eternity will begin once again in peace"
De Blob's Transformation Engines send out a wave of positive energy that helps restore the color and plants of all the neighboring areas and gets rid of the gloomy gray sky.
In The Legend of Zelda: The Minish Cap, once Vaati is defeated and Zelda wishes for everything to be back to normal, you see all the enemies vanishing from existance across Hyrule. Hyrule Castle is also repaired and returned to normal, and all the guards are turned back from being stone. It's even described as a miracle.
In Prince of Persia (2008), healing one of the fertile grounds results in a wave that wipes out the corrupted ruins revealing... well, still ruins, but nice ruins overgrown with greenery.
Using the Bloom power on a Guardian Sapling in Ōkami results in a wave of flowers that removes the curse from the area.
At the end of Lunar: The Silver Star, large parts of the world have had all life sucked from them and the main hero is gone, then this happens.
At the end of The Legend of Spyro: Dawn of the Dragon, Spyro uses his full power loose one to reverse the destruction of the world caused by the Destroyer. Though it seems to be a Heroic Sacrifice at first, it turns out he and Cynder both survive.
The AGD King's Quest IIIFan Remake: If you are able to get a certain item, then it will create this effect over the dragon-ravaged Daventry at the end.
Your ultimate reward for reaching the center of the Galaxy in Spore is the Staff of Life, which allows you to create a wave of green energy that instantly transforms a barren planet into a thriving terraformed world. You can only use it 42 times, though.
In World of Warcraft, the re-origination device in Uldum is basically this - except that it doubles as a Reset Button. It purges all impurities and returns the world to a "virgin" state — hence getting rid of everyone, both good and bad. Needless to say for most mortals they believe the world isn't that far gone, so the struggle is keep it from going off.
Somewhat cynically used in Gears of War 3. The Imulsion was parasitic and the Lambent forces were merely an extension of that, most everything on the planet had some degree of contamination. Adam Fenix devised a pulse generating machine to neutralize the Lambent and in doing so it couldn't descriminate against the Imulsion in any living being, including Locust or Humans. Because the Locust had so much longer exposure to Imulsion they are virtually wiped out in the process. Humans who spent an inordinate amount of time with Imulsion were also killed, including Adam himself.
In Bastion, this is invoked but deconstructed in the Restoration ending. The Bastion completely resets the world, so the characters are replaced with their past selves, and there is nothing to stop events from repeating themselves.
On a somewhat smaller scale, in Crysis 2 you hack the alien bioweapon to instead spread a wave of the anti-virus through New York, instantly killing the aliens and seemingly curing the diseased humans.
Averted in Final Fantasy VI. Although killing Kefka stops the gradual extinction of all life on the planet, and turns the sky and ocean blue again, the world is still in ruins. With the symbolism of flowers blossoming, doves flying, and a baby being born, it's at least strongly implied that the world will recover.
Occurs in the first, second and last levels of Flower. Particularly in the last level, you are the healing wave!
Activating the Crucible in Mass Effect 3 makes it do this to Earth, with Shepard's decisions changing the exact nature of the wave itself, but all of them result in the Reapers' systems being fundamentally changed forever. Have a poor enough Effective Military Status, and it becomes a world-killing wave as it fires indiscriminately, wiping out all life on Earth.
It's possible the world healing wave turned all petrified people back to normal, as opposed to just undoing what Trigon had done. Terra was turned to stone before Trigon came to earth, and this spell could explain why she came back
The VeggieTales episode "Lord of the Beans" ends with the hero creating one of these with a magic bean thrown into a dry well.
Minor one in Generator Rex, when Six's previous mentor dies, his body changes into some kind of energy and causes vegetation life to grow.
In the series finale, Rex uses the united Meta-Nanites' power to initiate a Global Cure Event, sending a wave of energy across the world that ends the Nanite threat forever.
In My Little Pony: Friendship Is Magic, "The Return of Harmony Part 1", Twilight Sparkle tries to cancel out the bizzare weather caused by Discord... it fails... miserably. In part 2, when the Elements of Harmony are unleashed on Discord, it not only turns him to stone but lets loose a World Healing Wave that restores Equestria to how it was before Discord appeared.
At the end of Xiaolin Showdowns first season, Wuya's return to physical form causes the surrounding region to decay. When she is imprisoned in a puzzle box again near the beginning of the second season, a World-Healing Wave occures.
In The Transformers episode "The Return of Optimus Prime, Part 2", a Hate Plague is spreading across the galaxy that fills everyone it infects with uncontrollable rage. In a last attempt to stop it, Optimus Prime releases all the wisdom contained within the Matrix of Leadership, which not only cleanses Earth, and quite possibly the entire galaxy, but also leaves everyone a little wiser than they were before.
In Transformers Prime, we get the Omega Lock. With the four keys in place, it can create one of these and revive Cybertron. However, Megatron wanted to direct it at Earth and "cyberform" it, overwriting what was already there with a new biosphere suitable for Transformers. Like the Star Trek franchise's Genesis device, the difference between a World-Healing Wave and a World-Wrecking Wave can come down to whether or not that world had anything on it beforehand. Optimus was forced to strike the Omega Lock with the Star Saber, possibly ending any chance of ever reviving Cybertron. In the season 3 finale, a rebuilt but weaker Omega Lock is used to revitalize Cybertron's core. It's technically a world-healing wave, in that it brought the planet back to life, but it isn't powerful enough to fix all the surface damage. Better than nothing, though.
Taken to its logical extreme in the Mortis trilogy of Star Wars: The Clone Wars, where the healing and wrecking wave are following eachother in a constant circle, as part of the planet's Light and Dark in-balance symbolism: when night falls all plants die, and are reduced into ghastly glowing forms, and massive thunder storms start. When dawn approaches all plant life is renewed.
The titular Captain Planet tended to act as a localized anthropomorphic version at the end of any given episode of the series that bears his name, cleaning up whatever pollution the villains had caused. This leads to a bit of Fridge Logic: why NOT pollute when a magical mullet man can clean it all up instantly?