Played with in Slayers: Divine Magic draws its power from the gods of the Slayers universe (as opposed to Demonic Magic and lesser Black Magic, which is powered by demons), but it was lost a thousand years ago and the few characters who use it (dragons and their associates, like Lina's sister, etc) are generally not inclined to. Sample spells? Chaotic Disintegrate and Flame Breath. The lesser form, White Magic is supposed to be entirely made of healing, protection or at least exorcism spells, and dismissed outright as a possible weapon by more sane mages like Lina and Zelgadis, but cranky Martial Pacifist characters still manage to use it against Always Chaotic Evil foes (Good Hurts Evil) in what Zelgadis called "oxymoronic attacks":
Most of the weapons used by the Magdalene Order of Exorcists in Chrono Crusade are some form of Holy Hand Grenades. There's holy ammunition in the form of Sacreds (regular bullets with holy oil inside to act as a small explosive) and the more powerful Gospels (bullets made with alchemical silver, inscribed with holy runes, and packed with holy oil), a sword in which the handle is a cross and the blade is made out of some sort of holy energy, etc.
Vento of the Front has "God's Divine Punishment", which causes everyone who feels hostility towards her to suffocate.
Terra of the Left's "Execution of the Light", drawn from Jesus' execution on the cross, alters the hierarchy of objects around him and alters their vulnerability.
Acqua of the Back has "Divine Mother's Mercy". It erases the Original Sin and allows him to remove all his biological limiters, use magic (specifically water magic on a mass scale), and No Sell practically any attack thrown at him.
It's eventually revealed that Touma's Imagine Breaker is of divine origin and sealing something ludicrously powerful inside Touma.
In D.Gray-Man, Exorcists fight using weapons made of a substance called Innocence, which is said to be 'God's crystal'.
While not specifically holy in nature, in GaoGaiGar Mamoru's purification abilities are mostly used to turn Zonder cores back into the humans they were made from, as well as counter the mechanization process in general. In FINAL, however, Mamoru shows that they are potent enough to utterly vaporize his target if he dials the power up high enough. Earlier in the series, Replica Mamoru also demonstrated considerable destructive power with his own abilities, though his powers stem from a different source and may not count.
In Fairy Tail, the Magic Council has Etherion, an extremely powerful magical weapon, with which they would have sacrificed innocent people to prevent the R-System from being completed.
Also Makarov and Laxus' spell Fairy Law, which creates a blast of pure light that annihilates those who are considered "foes" by the casters' heart.
In Saint Beast, Judas wields a very destructive force of light.
White magic in Magic: The Gathering qualifies, including mass destruction spells like "Fire and Brimstone," "Armageddon," and "Wrath of God". Evidently Richard Garfield applied the Old Testament to that element.
This is particularly clear with some white spot removal spells, like Devouring Light and Smite, whose theme clashes with less-aggressive removal spells like Pacifism, Oblivion Ring and Journey to Nowhere (that despite the ominous name seems to depict the creature affected by it as being sent to, very literally, a better place).
The Mighty Thor was once hit by his own Hammer. It had no effect, because the Hammer can only be used for good.
In Hellboy: The Crooked Man, an elderly preacher take a demonic lucky charm and proceeds to (in his own words) "squeeze the Holy Spirit into it". He then uses the charm to draw a cross onto a shovel, which he gives to Hellboy to bash a demon over the head with.
Played with in Justice League Elite. Manitou Raven's magic axe is incapable of piercing the skin of an innocent. It can, however, pierce Green Arrow's skin, because he's sleeping with Manitou's wife. Manitou uses this to save Green Arrow's life when he nearly falls to his death, by embedding the hatchet in his chest and using it to pull him up. After Manitou's death, Dawn gives the axe to the devout Muslim Al-Sheikh.
Hellboy's gun fires all sorts of religious Depleted Phlebotinum Shells, including shells filled with Holy Water, White Oak shavings and garlic, while the gun itself is made of metal from church bells, crucifixes, and pieces of the True Cross.
TRON's Deadly Disc became one of these after some upgrades from Alan. Seeing as Users are considered the equivalent of Gods to the Programs inhabiting cyberspace...
Atypical in that half of those listed served to demonstrate the ineffectiveness of the Egyptian gods (each of the Ten Plagues directly attacked domains central to the various deities of Egyptian polytheism), and that the most commonly referenced pillar of fire was never used offensively.
While there certainly are Holy Hand Grenade moments in the Old Testament, they're actually not that common, especially not after the Exodus. Those who think the Old Testament is all floods and plagues clearly haven't read it.
When Elisha was mocked by a group of youth, he cursed them in the name of the Lord, resulting in 42 of them being mauled by bears.
Also, the walls of Jericho were taken down by seven days of trumpeting and God's very own intervention.
Not that it was ever used offensively, but the Ark of the Covenant had wooden handles because anyone that touched it directly was killed as though struck by lightning. This combines with the design of the Ark to make some think it was an electrical generator or something, possibly with sparks arcing between the two angel statues when in use.
The primary violent methods for heavenly powers to interact with the mortal world has been through three swords that are supernaturally good at cutting up things because each one is endowed with a single nail that pierced Jesus to the Cross. Note that Fidelaccius, the Sword of Faith, is able to slice through a Red Court Lord of the Outer Night with a single blow. Amoracchius, the Sowrd of Love, cut through the arm of the Red King and shielded the wielder's child from harm. Simply put, the Swords are hardcore holy weapons. The RPG makes it clear: by paying a fate point the Swords can satisfy any "catch" that an enemy's toughness or recovery powers have. Note also that the Power in each of these Swords lays not in the physical vessel, but in the ideal aligned with the blade. So even if the vessel of the Power is broken, the Sword is not beyond repair. The Swords can even take forms which aren't typical for a sword. This allowed for Waldo Butters to reconstitute the broken Fidelaccius not as a katana but as a blade of angelic light and choral hum. This made it essentially a lightsaber.
The other is Soulfire, the Fires of Creation wielded by Him and His angels acts asa form of magic booster that was first see used by a wizard to burn part of his soul in exchange for dramatically improving the power and complexity of his spells. While less violent than, say, giant bursts of hellish flame, very much not White Magician Girl material. It is so potent to the corrupt, that when a typically quick healing Denarian, human playing host to a Fallen Angel, was injured by Soulfire he remained crippled several hours later.
Sunlight in a handkerchief is a potent, if limited battery, weapon against the Red Court. The catch is that you have to be genuinely happy to make it.
Faith is a vaguely defined power that seems to be able to repel some forms of evil creatures and Fae. One Knight of the Cross named Michael, wielder of Amoracchius wore a cloak with crosses embroidered onto it. A Red Court vampire touched it and was set on fire.
More humorously, water balloons filled with holy water are also an effective weapon against vampires.
Shadows of the Apt: In Salute the Dark, while all past indications have been that Butterfly-kinden are utterly harmless and completely abhorrent of violence, when Salma is killed, Prized of Dragons feels hatred for the first time on her life and uses her Art to incinerate the Wasp-kinden responsible in a blinding flash of light.
In Under the Dome, Chef Bushey has an AK-47 with the words "God's Warrior" painted on the side. He believes that protecting his meth lab is the will of God, and he is willing to go to any extreme to do it.
And, of course, there is the one in Discworld. A preacher who walks across Uberwald with Forgiveness in his hands. Forgiveness is a battle axe.
In Robert E. Howard's Conan the Barbarian story "The Phoenix on the Sword", the mark of the phoenix is put on Conan's sword by Epimetrius, which lets Conan slay the demon that Thoth-Amon summoned as revenge against Ascalante, even after the sword is broken during the battle with Ascalante and his assassins. The phoenix mark is identified by the high priest of Mitra.
In Special Circumstances, A warrior's "aspect" basically serves this trope's purpose. Most supernatural beasties can only be killed when a warrior calls on their beliefs while in combat with them.
The Young Wizards series has the four great treasures of Ireland, where each treasure is an object which houses a powerful holy spiritual entity which have various Elemental Powers. In particular, the Spear of Light acts as the "body" for the Virtue of Fire, which as the embodiment of purification is particularly harmful to evil.
In Heralds of Valdemar, there's Final Strike in which the user pulls all the life-energy in the area through his own body, resulting in a massive explosion. The magic user doesn't have to be very powerful to do this, although the more powerful she or he is, the bigger the explosion; the person does not survive the experience, of course.
Live Action Television
In Power Rangers in Space, the Red Ranger is forced to resort to killing Zordon. Doing so unleashes a wave of goodness across the universe - all currently attacking evil monsters are turned to dust, all currently attacking humanoid villains are turned good. That makes Zordon a holy universal nuke.
In Supernatural there is a rather literal example of this trope where Castiel uses a molotov cocktail full of holy oil to take out Michael, if only for a few minutes.
Many higher tier angels have this ability, the most predominate example being Raphael.
There are various instances in which goodness represented by an object repels evil in folklore. Vampires, for example, are supposed to be weak to holy water, communion bread, crucifixes, etc. Unicorns were often said to be vicious, behaviorally monstrous beasts capable of being tamed only by the touch of a purehearted maiden. And so on.
One of the more noteworthy spells in a 3.5 edition supplement was the Bolt of Glory which fits this trope to a tee. A clerical attack spell with the Good subtype that deals heavy damage to evil outsiders and undead, and could still pack a whallop to anyone but holy outsiders.
In Fourth Edition, clerics have even more spells that can do damage to just about any kind of creature. Clerics who specialize in these are nicknamed "Laser Clerics."
Also in Fourth Edition, there is the Avenger class, which is a class pretty much devoted to this trope. Slightly subverted in that unlike other divine classes, Avengers are always allowed to be unaligned, regardless of the affiliation of the god they serve. Paladins also have very strong ties to this trope.
Book Of Exalted Deeds is a supplement for 3rd Ed. that is just full of this trope. It starts from the basic premise that people need to play better characters, in the moral sense, and does a fine job for a while — and then you get to the Ravages and Afflictions. See, if Poison Is Evil, then Good Guys can't use it. However, Ravages and Afflictions are poisons that only hurt Evil characters, so they're okay! Some of the stuff in there is awesome — just not the Holy Hand Grenade part.
Most good stuff was converted from earlierbooks of Planescape. Warriors of Heaven — note that its author participated in BoED too — already had magic mostly restricted to Celestials and whoever they deem really worthy, including attacks. Parts designated "only good guys" weirdly (like telepathic eavesdropping) or reminding of "12 yr old gamer girl" template from Portable Hole are new additions.
Also, the Ecclesiarch (high priest/Pope type) has a rosarius that projects a force-field. Not a weapon as such, but not what you would expect a priest to be carrying. Of course, in 40k, practically everything in the Imperium is holy, and practically everything could be and is used as a weapon. Imperial Priests also often carry a two-handedchainsword known as an Eviscerator.
The Dreadnoughts are a fine example of this. A tomb-cum-shrine, with legs, a massive machine gun and a missile launcher.
A number of the Space Marines might consider all their weaponry of this nature, though it probably isn't by the nature of the setting. Depending on how zealous they are, certain Imperial Guard regiments might have the same attitude toward their equipment.
This will definitely be the view of the masses towards Space Marine equipment, as they're commonly indoctrinated to believe that the Astartes are literally the angels of the Emperor responsible for bringing death to the Imperium's enemies.
Celestial Exalted get a lot of Charms with effects like this. (Terrestrials also have one or two, but they're much less potent, and are relatively recent creations, developed to compensate for the fact that they usurped, exterminated, and then demonized the remnants of the Exalted with real holy power.) There's also the Solar Circle Sorcery spell Light of Solar Cleansing, which nukes any "Creatures of Darkness" in the area, leaving everything else untouched.
Which is not to be confused with Cleansing Solar Flames, another Solar level spell that destroys shadowlands.
Wonders of the Lost Age (the Magiteksourcebook) introduces the Sun's Fist Chakram, a literal Holy Hand Grenade.
Warhammer Fantasy battle and roleplay has the gods of the empire to mainly help their followers.....until they decide to unleash destructive powers rivaling those of mighty sorcerers. Brettonia avoids this by having their goddess only protect the knights from harm and give them powers when they become epitomes of good, the destructive power of their "damsels" (mystical priestesses) are given by training from elves.
Deadlands and its CCG counterpart, Doomtown, have the Holy Wheel Gun, a revolver with "The Right Hand of God" engraved on the barrel. It does terrible things to monsters, especially the more profane, like the walking dead, werewolves, and vampires.
Stats for the Holy Hand Grenade itself are given in GURPS Camelot.
Ironclaw the Church of s'Allumer has a few offensive holy spells, such as Fulguration, which is too dangerous to be readied bare-handed and must be cast with a rod, wand, or calendar sword. And then there's the Lutarist faith's Blessed magic, which is not supposed to be used to attack and punishes the user if they do so.
The Light Element in BIONICLE. Examples include Takanuva and Av-Matoran.
The Apple of Eden in Assassin's Creed is a Holy Hand Grenade. The main difference is that it is actually a long lost piece of technological equipment created by an older, much more advanced civilization on Earth, who used the Apples of Eden to enslave humanity.
Joshua's attacks in The World Ends with You, several of which involve casting beams of holy light surrounded by cherub angels.
In most of the games, and a few other Square Enix series, "Holy" is often equal to "Flare" in terms of effect and damage. In the days Nintendo had censorship policies, Holy was given different names, like "Fade" in Final Fantasy I, "Pearl" in Final Fantasy VI and "White" in Final Fantasy IV and a handful of others.
In addition to Holy, Final Fantasy I also included the Dia series of spells, initially translated as "Harm". Dia's power only affects undead creatures, but it causes heavy damage to them. Later games did away with Dia and instead implemented the rule that Revive Kills Zombie.
Final Fantasy XI brings the Dia series of spells back, though the first Dia is the lowest level white magic available. Instead of straight-up Holy damage, it does light elemental damage over time and lowers the target's defense. Still extra harmful to undead, but it damages everything else just fine.
The early games had a cross necklace as an item. When picked up, it creates a bright flash of light that kills everything on-screen.
Ragnarok Online has the Holy element which is extremely resistant to Earth, Water, Air, Fire, Poison, and Ghost attacks, but was both weak when attacked by and strong in attacking Shadow and Undead.
Master of Magic has Life magic, their offensive spells only work on creatures of Chaos, Death or summoned creatures though. Their BENEFICIAL spells makes it probably the most powerful magic in the game.
Word. Life-backed armies get buffs out the wazoo. Beware of even the humblest spearman unit buffed with Heroism, Invulnerability, Righteousness, Holy Armour, Holy Weapon, Lionheart, Crusade, Charm of Life and a stacked Prayer/High Prayer - not to mention getting Healed even if you do manage to damage them. Heroes, meanwhile, not only get all these benefits but can be Resurrected as well!
World of Warcraft has the Holy school of magic, performed exclusively by priests and paladins. While most Holy spells are for healing or buffing, there are a few damage spells and a Holy DPS priest makes a viable—if challenging and unorthodox—character option. What's nice about holy damage is that there's no resistance or immunity to it, at the cost of dealing slightly less damage than the other schools.
This is even more true since "Mists Of Pandaria" gave Paladins an overhaul. Many Paladin abilities now either generate Holy Power or are fueled by it. All Paladins use holy power, and Retribution Paladins specifically use it as a weapon.
Crono in Chrono Trigger uses "Heavens" element magic. This is why he learns Life, and makes two pairs of opposing elements (Fire and Water, Holy and Shadow), but the English version names it Lightning (since some of his attacks and multitechs cause lightning to strike from the heavens) instead. Luminaire is the best example of this trope. The DS version renames his brand of magic "Light" magic, bringing it closer to the original Japanese naming.
Grandia II plays this straight with Elena's ultimate move, White Apocalypse.
A few units in the strategy game Age of Wonders can deal Holy damage, which is a useful damage type in that it has a chance to cripple enemies with the Vertigo debuff. Most spells that deal Holy damage are from the Life sphere of magic, and the incorruptible, quasi-angelic High Men race has several units that deal holy damage in melee or from afar, the earliest example being the Saint unit, which can fling Holy Bolts as an effective ranged attack.
In sequels Archons (High Men stand-in) do it again, as well as Good priests and summoned units like Angel.
Seiken Densetsu 3 has light magic as one of its 8 elements, with spells like Saint Beam and Silver Dart. It is unique among the 8 elements in that it utilizes your Spirit stat, instead of Intelligence.
Nexus War is all over this trope. Evil may have the dirty tricks, but Good has all the big guns. Embracing the holy love and peace of Paradise lets characters turn into firestorms, throw cars and trees, replace limbs with weapons and summon holy war machines. Let's not even get started on all the smiting. When Heaven goes to war, it goes to war.
One of the random encounters in Fallout 2 is with a bunch of knights in power armor looking for the Holy Hand Grenade. Another random encounter features actual grenade itself, but it is regrettably unreachable due to script error.
In fact, even Fire Emblem Awakening and Fire Emblem Akaneia, which don't have the above mentioned Elemental Rock Paper Scissors, do have the Book of Naga and the Aura and Starlight tomes, respectively.
Guild Wars has smiting prayers in general, and Ray of Judgment in particular, which is arguably the most powerful spell against a stationary target.
The mikos of Touhou do this quite a bit. In fact, even the goddesses they worship themselves aren't averse to rolling up their sleeves and getting into brawls using their "miracle" power to level massive destruction at whatever random Gensokyo resident they feel like fighting with at the time. Inaba of the Moon & Inaba of the Earth gives the ShoutOuts to Monty Python and Wizardry by mentioning the HHG of Aunty Ock. Another specific example are the Celestials, whose very body is anathematic to the Youkai. Too bad the only playable Celestial is a colossal Jerk Ass.
Champions Online offers the Celestial powerset with the Blood Moon content, focusing primarily on abilities that can both damage enemies and heal allies. There are a few individual abilities in other powersets as well, particularly Condemn in the Supernatural set which hits the enemy with a column of light from the sky and can stun enemies near the point of impact.
This is the shtick of three of the four Priest subclasses, especially the Crusader, in Dungeon Fighter Online.
The Tales Series games has had Light-element attacks, like Photon, Holy Lance, and Judgment, since the very beginning. And despite it being a lightning-based spell, the Indignation spell fits under this trope; the incantation describes the caster as commanding heavenly powers to send down "Divine Lightning"; when the spell is cast, the skies part and lightning falls from the heavens. In some games it is a proper light elemental spell.
The Tales of Legendia spell God Press (incorrectly localized as Judgement) hits enemies with an actual holy hand.
Church Militant Ciel from Tsukihime wields the Seventh Holy Scripture, a unicorn horn fused with the soul of a sacrificed girl. Clearly, however, this wasn't good enough for her, so she modified it into a pilebunker. It's so powerful that it can stop the reincarnation of a Dead Apostle, INCLUDING Roa. Or, rather, it's specifically designed to stop the reincarnation of one such as Roa, and happens to stop reincarnation by any lesser being. It's filled with the power of all church verses, theories, sermons, etc, that deny reincarnation, imparting that belief upon the one hit.
All of the Church Executors (among which Ciel is a member of the elite Burial Agency) in the Nasuverse are capable of using weapons powered by faith, the most widespread of which are the Keys of Providence, who have the ability to impose natural laws on their targets (for a vampire this means their body is forcibly brought back to human. Dead human, with the additional effect of falling to dust if the vampire is old enough) and, in case of the blade-like Black Keys (the most seen type of Key of Providence), stopping them cold if they hit their shadows.
Worms has a literal Holy Hand Grenade◊ just like in Monty Python and the Holy Grail. A "HAAAALELUJAH!" choir sounds in the air, and immediately after that, sweet mass destruction is the outcome.
As a Shout-Out in Team Fortress 2, those who bought Worms Reloaded before its release get a promotional helmet for the Soldier. Holy Hand Grenades included. Taunting with the Equalizer will result in an "HAAAALELUJAH!" choir playing in the air, and foes too close will be reduced to tiny bits... in addition to yourself.
In Doom II RPG there's the Holy Water Pistol which makes most demons empty their bowels with fear(not literally), and to all Lost Soul variants, it does critical damage.
In Dragon Quest IX, the final ability of the Paladin, Solar Flair, is a light type ability that does respectable damage. Even better, the spell doesn't work off of Magical Might (the offensive spell stat), but Magical Mending (the healing spell stat). Since the ability can be given to any class, to any member once unlocked, it is the perfect move to give to the Priest, who has the highest Mending, yet not an offensive ability to speak of, so it's right at home with them.
The Plasma Grenades in Halo, which the Covenant refer to as "holy flare", "prophet's flare", or "cleansing flame" (Or "Demon flare", when thrown by an enemy). They're actually more akin to Sticky Bomb than this trope, though, but they're holy as far as the Covenant are concerned. Given that the Covenant reverse engineers Forerunner tech for all of their gear, and they worship the Forerunners as gods, it might still be literal truth to them.
Fate Cards in Septerra Core - magic cards attributed to one of four main gods of Septtera mythology - Marduk, Gemma, Dogo and Kyra and combining specific cards can dwell more into this territory:
combining specific cards with summoning card allows you to summon Marduk, Gemma and lesser mythological or legendary figures to attack your enemy or Kyra to heal the target and damage the undead enemies. Dogo's primary card - Joker - gives you random summon.
Combining two primal cards of Marduk and Gemma - Law (removes all negative effects from the target) and Chaos (target turns berserk and may attack it's allies) unleashes destructive power upon your enemy. Combining them with Mirror will create black hole.
The offensive Miracles in Dark Souls "Wrath of the Gods" and "Emit Force" basically channel your Faith into big explosions. Divine weapons are also the only things that can put down true Undead like skeletons permanently without killing the necromancer animating them first.
Anyone playing a Guardian in Guild Wars 2 will end up relying heavily on skills of this type. While there is no "holy" type damage in the game, a lot of their skills heal allies while simultaneously damaging enemies, and sometimes even setting them on fire. A Guardian's user interface will even periodically burn with blue flames to indicate that their passive buff skills are in effect. Interestingly, even nearby allies will have THEIR skill bar ignited with blue flames when they receive a buff from the Guardian.
Shows up in the Epic Battle Fantasy series as the Holy element. The page image is the cutscene from Natalie's Genesis Limit Break in the fourth game, which blasts enemies for a lot of Holy damage, heals the party, and revives any dead members. Natalie also gets the Judgement spell, which is Holy-elemental and has the greatest damage output of any single-target spell.
Board Game Online has a literal Holy Hand Grenade, attainable by combining Holy Water with a mundane grenade. They are noticeably more potent than their mundane cousins, with higher knockback and a bigger kill radius.
Minnie Mouse of all people in Kingdom Hearts II, actually has two variants: one a ball of light she projects at enemies that approach her, the other a combo attack with Sora which creates an explosion of light that fairly heavily damages enemies.
In Shadow Hearts, Alice has Blessed Light and Advent as her only attacks, with Advent being the most powerful elemental attack in the series. Yuri's Light-based fusions and several Light-based enemies also have fairly powerful Light attacks.
In the sequel, Nicolai also has powerful Light elemental attacks.
Diablo II's Paladin class has a few abilities like this, most notably Holy Bolt and Fist of the Heavens. The Crusader class in Diablo III also has Fist of the Heavens—but, counter to the trope, that is now primarily a Lightning ability. The Crusader does have several other Holy abilities to make up for it, though, some of which are based off the Paladin abilities in World of Warcraft.
Much the same applies to its direct descendant, the Elements of Harmony in My Little Pony: Friendship Is Magic. Although its first use is to dispel dark magic rather than inflict serious harm, its second shot petrifies a being of pure chaos energy. Bastard had it coming, too.
The Crystal Heart, empowered by the joy of the revitalized Crystal Ponies, sends out a burst of light that shatters the Evil Overlord unicorn whose soul had long since collapsed into darkness.
Energybending in Avatar: The Last Airbender, being not only the original and thus purest form of bending, but also implied to be divine in origin, what with having origins in the spiritual world and being used solely by the Avatar. In the Sequel Series, The Legend of Korra, Amon claims to have adquired what appears to be the exact same thing from the spirits. It turns out to be a combination of bloodbending and chi blocking. And it still isn't as powerful as energybending, as Korra was able to reverse the effect with it.
In Hellboy Animated: Blood and Iron, Professor Bruttenholm flings holy water at the vampire Erszebet Ondrushku, which burns her and drives her away. Later, when she takes a Blood Bath, Bruttenholm spikes it with more holy water, and this kills her.