In the animated Hellsing, this is how Alucard defeats Incognito: he uses his cross-melting aura to make a long silver stake to impale Incognito on: first through the chest and heart, then vertically all the way through.
In Naruto, the First Hokage's necklage is able to contain the Ninetails/Kyuubi inside him when he manifests up to four tails. Beyond that though...
Dracula's brides make Jonathan Harker's cross liquefy off his body as they seduce and drain him. Thankfully the process seems not to have superheated it, as it flowed off his chest harmlessly. It was a small cross; not enough power to ward them off (the bride that melts it recoils for a bit before regaining her composure and working her magic).
Subverted with the vampiric Lucy as she most likely isn't powerful enough to go against crosses (being newly turned an all).
Played straight against Dracula who burns the cross Helsing tries to use against him.
The original has scary-movie actor turned vampire hunter Peter Vincent tries to use a cross against the vampire. The vampire takes it away from him and tosses it, noting that since Vincent doesn't believe it will work, it won't. Charley tries it, using a much smaller cross. His greater faith actually causes Jerry to cringe away.
The remake has this occur has a crowning moment of snark when Charley tries it on Jerry:
Jerry is cringing and staggering backward from the cross Charley is brandishing at him. Jerry: No, not the cross, Charley, not the cross... (Jerry grabs the cross as soon as Charley's in reaching distance, invoking the trope) cross catches fire and crumbles Jerry: No, Charley; not the cross.
In Dracula (1979), Jonathan Harker tries to ward off the Count with a wooden cross, but he just smiles and grabs it, making it burst in flames.
Wherever the rosary touched the bag above the fungal glop, a thin trickle of grey smoke rose up into the still apartment air. "Looks like that'll kill it", Simon said. [...] It wasn't the fungus that was on fire after all. It was the rosary.
In the Eisenhorn book Hereticus, a priest mistakes Cherubael for a manifestation of the God-Emperor and runs to meet it with an Imperial aquila. While the aquila manages to keep Cherubael away at first, eventually the daemonhost manages to melt the aquila.
Happens again in 'Salem's Lot, when Callahan's faith falters when confronting the ancient vampire Barlow: when agreeing to toss aside his cross to save Mark Petrie, he hesitates, and the cross loses its power. Later in the same continuity (or at least partly), in The Dark Tower novel Song of Susannah, Callahan has gained confidence and knows the proper answer to such a challenge: he doesn't need to throw the cross away, but he can tuck it away and still retain the power of faith radiating from him and hurting the vampires.
Played with the sun itself by Tolkien. Throughout Lord of the Rings we've been told that the forces of Sauron like Orcs, Trolls and Nazgūl are afraid of the sun, and sunlight weakens or outright destroys them. And in the third book, we see Sauron's army on the march to Minas Tirith. Cue the sun fading and the day becoming dark as night.
Subverted in the third book, Grave Peril. While attending a vampire ball, a Red Court vampire (less vulnerable to faith than the undead Black Court) laughs at Michael's cross and grabs it mockingly, saying that it was immune to such things. The vampire then immediately bursts into white flame.
Of course it can be played straight depending on the person. In the Dresdenverse holy symbols only work if the person who is using it to protect himself actually has faith in what the symbol stands for. So a cross held by someone who has no faith is only holding a useless trinket. In Michael's case, he is literally a holy warrior chosen by god.
When Harry needs to use something, he uses the pentacle given to him by his mother. To him, it represents his faith in magic guided by human will.
All faeries are burned horribly by the touch of iron. All faeries except Mother Winter. She has iron teeth.
Both the book and film version of The Keep, have a version of this although in slightly different circumstances. In both cases there is a case where one of the officers holds up a cross to ward off Molassar the vampire. Who is actually not a vampire at all but a sort of Emotion Eater who predates written history. Both times there is a brief moment where it seems to be working, and then Molassar reaches out, grabs the cross, and effortlessly turns it into a twisted lump of metal. Rather more satisfying in the film version because it's happening to the Smug Snake SS Major instead of the noble, conflicted, My Country, Right or Wrong Wehrmacht Captain.
This is because the Haemovores are not actually repelled by holy symbols (like a cross), but rather the faith that their wielder has invested in them. As by this point in the story, the priest's faith is severely wavering, what power he may have had has simply seeped away...
There are numerous examples in Supernatural. Hallowed ground can repel minor demons, but not any that get named/affect the plot. Episode 4.09 I Know What you Did Last Summer features a statue of Mary bleeding from the eyes as the demon Alistair approaches.
The video for Dimmu Borgir's Sacrilegious Scorn has a priest threaten Shagrath with a wooden crucifix. Shagrath merely looks amused, grabs the crucifix, and sets it aflame.
The Baali in the Old World of Darkness. Being Satanist vampires, they are the only ones in the setting actually vulnerable to crosses (rather than to faith) but as they grow more powerful, they can repel religious people in turn.
Being the inverse of the Zenith Caste, Midnight Caste Abyssals in Exalted have the ability to toughen themselves against holy beings. This can also, more literally, be a result of Abyssal Resonance eruptions. Lastly, a class of First Circle Demons called teodozjia are basically hardcore Yozi priests, and engage in a battle of this vs. Good Hurts Evil if they come across a Zenith Caste Solar.
In Warhammer Fantasy, it's stated that when a priest shows a vampire his symbol, there's actually a battle of wills going on. if the priest wins, the emblem repels the vampire. if the vampire wins, well...
In the game The Darkness, the final part of the game seems to involve the eponymous Darkness (which is generally weakened by light) supercharging due to a solar eclipse. With the greatest source of its weakness blotted out, it reaches a power level where it explodes lightbulbs that are near it, destroying both light sources and potential light sources.
In World of Warcraft, the suicide/lichification of Ras Frostwhisper by the Lich King is evil enough to corrupt the Stratholme Cathedral, remove its connection to the Holy Light, and consecrate it to the Scourge.
In King's Quest II: Romancing The Throne, the silver cross given to you by the monk will protect you from Dracula. But in the AGD InteractiveFan Remake, if you try the cross on his equivalent (the Affably Evil Count Caldaur), he'll kiss it and sarcastically say "God bless Daventry". (This may have a little something to do with the fact that the monk is evil in this version...)
Dracula in Castlevania: Lords of Shadow 2 creates one after (failing to) break a paladin he just bested with a Reason You Suck Speech. And just to drive the point home, he begins to chant the same Latin prayer that the paladin's chanting. The end result is a cross melting aura that causes such a massive explosion of power it can be seen from space and also destroys his 100-something acre castle. When it clears up, Dracula's standing in an empty field of nothing but ashes with a molten red crucifix and a rather confused look on his face. In this case, it's not because he's too powerful or evil for the cross, it's because he is still God's chosen champion.
May appear in Sluggy Freelance, in "Vampires". Riff, being Jewish, uses a Star of David against vampires, since any holy symbol will do. (They even consider a can of beer, but not light beer.) The powerful Lysinda Circle vampire Valerie grabs the symbol from around his neck and crushes it; she doesn't seem harmed by it at all, and while she's touching it, there's a hissing noise. It could be some version of this trope, though it might also be that it's actually burning her, but to such a small extent that she's able to ignore it.