In The Parselmouth of Gryffindor, Maximilian, a Boggart-turned-human, is still weak to the Riddikulus Curse (to the exclusion of nearly all other curses), which is useless on any other creature.
In Power Girl story A Force of Four, Badra and her Kryptonian allies banish all magic from Earth before setting their plans in motion. And since there's barely Kryptonite on Earth-Two, the heroes have barely any means to stop them.
In Supergirl story Hellsister Trilogy, Satan Girl considers her options to exterminate the inhabitants of Daxam and Rokyn: lead for Daxamites and magic for Kryptonians since Kryptonite will not work in a red-sun world, except for a hard-to-make variety.
Last Child of Krypton: Revealed when Gendo pulls a piece of kryptonite out on Shinji -who is Superman in this crossover- after the Bardiel incident.
Superwomen of Eva 2: Lone Heir of Krypton: Asuka discovered she was half-kryptonian at the same time she found out about her weakness towards kryptonite. Shortly after Gendo stole the piece of kryptonite and he threatened her with it several times.
A Star Wars version here The Princess And The Pirate. The Imperial-aligned captors of Luke, Leia and Han put them in a room with some kind of small, furry mammalian creatures that somehow sap the two Force users' power and prevent them breaking out. Luke eventually solves the problem by killing them. However, it accidentally happens again later, when a young rebel thinks Leia would like one of the cute critters and lets it loose. Leia faints, but Luke's able to tell him to get it out of the area.
Referenced in the Star Wars/Stargate SG-1 crossover "Destiny's Child"; as Anubis learns more about the dimensionally-displaced USS Resolution, he muses that the ship's apparent phased energy weapons may actually be able to kill him even in his part-Ascended state if he was shot directly, as such a weapon could disrupt his energy matrix.
The Lightning Strike features an inversion of this where the hero renders the element useless; after Skye joins the Avengers, she learns that she can use her powers to negate the special abilities of vibranium, making her particularly useful to the Avengers as they hunt for any remaining Hydra forces.
In En Tempus Veritas, when Lois becomes pregnant with Clark's child, although the baby is only half-Kryptonian she and Clark are naturally reluctant to ‘test’ how exposure to kryptonite radiation would affect the pregnancy. At one point, Lois is forced to just watch after a mind-controlled Chloe leaves a lump of kryptonite on Clark’s chest until Martha arrives to take it away; Lois subsequently orders a lead apron so that she can be of more use if that scenario happens again.
In Wolverines, Wendigos and Winchesters, as well as the known demon weaknesses such as salt and holy water, adamantium is revealed to be particularly dangerous to them, as a demon’s wounds start burning the moment Logan stabs the man with his claws and the demon panics when Logan identifies the metal that they’re made of.
A Draconequus like Discord and his family are all Reality Warpers. However, they cannot directly affect anything created by taking away something. For example: ice (created by taking away heat), despair (created by taking away hope), and the vacuum of space (created by taking away air and matter). As a result, they can be imprisoned by ice and similar substances for a time (note that although they cannot poof away ice or transmute it, they can eventually generate enough heat to melt it or break free with brute force). They are also vulnerable to the Rainbow of Light and its present day counterpart the Elements of Harmony. As the Goddess of Harmony, Cadence is a Man of Kryptonite to them and even her blood can affect them negatively.
In Yugioh EQG: Shadow Gates, Shadow's deck, Shadow-Mechas, has monsters from the extra deck that all have the ability to reduce the attack points of the monster they are attacking to zero if it is the same type of monster as them (Fusion against Fusion, Synchro against Synchro or Xyz against Xyz).
Willow: Well, Supergirl ought to be safe from everything. Except maybe Kryptonite. Supergirl: No, Willow. Kryptonians are vulnerable to magic. If you performed the right spell, even you could hurt me. Willow: Then you mean, like... well... vampires... Supergirl: Yes, dear. Vampires can hurt me. The last time I met Buffy, they did, several times. But I go where the job takes me.
In The Institute Saga, Superman is prevented from directly participating in the final battle of the first story due to the sheer amount of Kryptonite that Magneto is using.
In To Hell and Back (Arrowverse), Kara and Kal found out they were vulnerable to Kryptonite during the time in the League of Assassins (though the exact specifics are a Noodle Incident). Nonetheless, Barry Allen designs Kryptonite-proof clothes which protect Kara from Kryptonite and allow her to use Kryptonite weapons against rogue Kryptonians.
Daily Equestria Life with Monster Girl: For some reason, the plastic hairpins and practice sword that Cerea brought from Earth to Menajeria now negate magic on contact. Unicorn spells and devices are negated, pegasi lose their flight, earth ponies and minotaurs grow sick and feel their strength leached away... every sapient on Menajeria has magic, and all of them have reason to fear and loathe that sword. Menajeria's technology has not yet reached the point of producing plastic from petrochemicals, so we don't know if native plastic would have the same effect or if it is unique to plastic that made the dimensional shift with Cerea.
. The Imperial-aligned captors of Luke, Leia and Han put them in a room with some kind of small, furry mammalian creatures that somehow sap the two Force users' power and prevent them breaking out. Luke eventually solves the problem by killing them. However, it accidentally happens again later, when a young rebel thinks Leia would like one of the cute critters and lets it loose. Leia faints, but Luke's able to tell him to get it out of the area.