"Superman could move planets, and most people that fought him were lucky if they had a working bike. To balance this out, as soon as they graduate from crime school, every single criminal in the universe is given an unlimited supply of kryptonite along with their retarded hat and matching retarded jumpsuit. Kryptonite is radioactive pieces of a planet that exploded decades ago on the other end of the universe, which might explain why it's so easy to find."
In One Piece, water is the weak point of all Devil Fruit users. And considering that nearly the entire maritime series takes place either at sea or on some tiny island... And then, the technology exists to condense the power of the sea into a stone-like material, which can be used in construction, weapons, handcuffs, etc. That seastone is supposedly rare, but its use has been prevalent enough to nearly warrant this trope on its own.
Seastone is actually naturally occurring, which is why it's so rare.
There are a few limitations in play, though. Only "standing" water that submerges at least half of your body counts. So things like light rain or drinking water are fine. It also helps that only half of the main cast are Devil Fruit users.
After the Time Skip in Naruto, all Sasuke has to do is make eye contact with someone to trap them inside an illusion. With this he can render his opponents immobile, make them think he's dead when he's actually about to attack them from behind, or just flat-out Mind Rape them. You'd think this would make him nearly unbeatable, but in every major fight he's had since getting these powers, his opponents have all either had years of training on how to resist this exact technique, had illusionary powers of their own that cancel out Sasuke's, or had Superpowered Evil Sides that can dispel illusions for them.
The fact that overuse of these powers ultimately leads him to blindness and probably loss of said powers and he by now already has a pretty bad eyesight doesn't help him either.
Most of the genjutsu-using protagonists face this problem. When Kurenai attempts to use genjutsu on Itachi, he reverses it onto her. When Fukasaku and Shima attempt to use their genjutsu on Pain, he survives it the first time, and interrupts it by stabbing Fukasaku the second time. This may be because genjutsu isn't considered a flashy enough way for the protagonists to win a legitimate, suspenseful battle, which may be why the villains use it more often. It has been useful against mooks and Mauve Shirts on occasion, as it working then wouldn't end the fight.
The Sharingan, which only works if the subject is looking into it, lends itself to potential weaknesses (for example, if the target lays down mist and closes his eyes while approaching the user, watches his feet to read his moves, uses shadow clones, or simply moves too quickly for them to react).
This also applies to Suigetsu's Hydration Technique. You'd think being able to avoid attacks by turning into water and thus practical immunity to physical attacks would give him a significant advantage, but so far his major fights have him facing opponents that either paralyze him via electrocution (Killer Bee and Darui) or could just overwhelm him a ridiculously strong energy attack (transformed Killer Bee).
Many of these examples can be considered justified by how critically important proper information on your opponent is shown to be, as many abilities can be totally counter with just a while to prepare. For instance, of all the opponents Sasuke faced with genjutsu-immunity, only Killer Bee was like that coincidentally: the Raikage had a good deal of information about Sasuke from his scouts (and developed counters to several of his other attacks based on that as well), Deidara was building up the immunity to fight Itachi (who used with the same genjutsu power), and Itachi was pretty much the exact opposite as Sasuke was the one who built up his genjutsu skills to avoid losing instantly.
Once Miroku joins InuYasha and gang, his Wind Tunnel - effectively a black hole in the palm of his hand - proves nearly impossible to use effectively thanks to the scores of poisonous insects which Naraku keeps handy and lends out freely to his flunkies and pawns for just such a purpose. This and the Wind Tunnel's other drawbacks (its broad and indiscriminately destructive range, and the fact that every use brings it closer to collapsing in on itself and killing him- it issupposed to be a curse) mean that Miroku rarely gets much opportunity to use his best weapon effectively, although there are several instances in which he demonstrates his willingness to open it up in spite of the danger... including one epic Determinator moment in which he ignored the massive amounts of poison he was taking in to try to get rid of the Big Bad for good, even after he began bleeding heavily from the eyes and mouth◊.
There is even a flash parody of this on YouTube where, after Inu-Yasha gets attacked by (a fake) Naraku, asks Miroku for help. Cut to Miroku sitting back in a chair, reading, while half-heartedly saying "Sorry, old bean. Would love to help but, you know, poison insects and all that." In other words this happens so often that he becomes The Load.
In the Ranma ˝ universe, the Hiryu Shoten HaFinishing Move tornado punch is immensely powerful, devastating, and conveniently disposes of the enemy by flinging him far, far away. The first time Ranma used it against a serious enemy (in fact, the opponent he had learned it for) recognized the steps immediately and thwarted it; the second not only recognized it, but reversed it and used it against Ranma; the third can fly without restrictions and is therefore immune to it. There's also the limitation that it can only be fired straight up in the air, making it very awkward to set up and use even before these other weaknesses come into play. Ranma had to juggle weaknesses and variations on the technique to make it useful against these foes.
The Hiryu Shoten Ha was a shout out to traditional martial arts manga; it's pretty much the only remotely non-goofball attack used by anyone ever. If it ever became a gamebreaker, it would utterly screw up not just the character of Ranma but the entire tone of the manga. (Plus each battle would last about one page.) That plus being flung far, far away isn't a problem for most of these guys...heck, Happosai enjoys it.
This is subverted in the OAV's, where Ranma improves the technique to the point that he can fire it horizontally, essentially giving him the power to SHOOT TORNADOES AT PEOPLE. This never happens in the manga.
Plus, there's the fact that water itself is a kryptonite for Ranma and other Jusenkyo-cursed characters, who turn from powerful martial artist into small and (relatively) helpless animals, or into weaker women (due to unfamiliarity with the body.) So of course there will be water everywhere throughout their encounters.
It's a crippling weakness when Rumiko Takahashi can milk some laughs or a plot point out of it. Ranma's shorter arms and legs in his female form was an issue for ONE fight, against Mousse (and only for about a couple minutes).
Ranma stated that his female form has the advantages of being more dexterous (lighter, faster and smaller) so it's not a weaker version of his male form, it's simply different.
Saint Seiya: Dragon Shiryuu's Rozan Shooryuuha leaves his heart exposed for a second, and an opponent can strike him there on that moment to finish him off. Guess what happens the first time he uses it on a series fight. Subverted in that it's only used against him once more, by Capricorn Shura. Double subverted in that the attack is The Worf Barrage and rarely does much anyway, aside from breaking his own shield.
In an odd way, the Phase-Shift Armor of Mobile Suit Gundam SEED fits this. The armor was developed for the Earth Alliance's five Gundams as protection against Z.A.F.T.'s basic machine guns from their GINNs. However, once Z.A.F.T. stole four of the five Gundams, beam weaponry started to become more commonplace and most mook suits are protected with either an Anti-Beam Shield or Laminate Armor to protect them from beam shots for a small amount of time.
Green Lantern Hal Jordan's Silver Age weakness? The color yellow. His Kryptonite really is just about everywhere. (Of course a veteran Green Lantern will know how to get around this, e.g. when facing yellow poison gas, they simply make a fan to blow it away.) It was made even more ridiculous by the fact that yellow was invoked in places where there clearly wasn't any, such as the moments when Hal would claim that he was failing because of a "yellow compound" or "invisible yellow" or even "infra-yellow" (especially as "infra-yellow" is in fact orange. He's vulnerable to two colours now?) At least it generally takes a little effort to find something that's both yellow and suitable for use as a weapon.
Alan Scott, the Golden Age Green Lantern, had a ring that couldn't affect wood. As Rajesh Koothrappali pointed out, you could kill both Green Lanterns with a number 2 pencil, while Cracked.com calls the banana tree "the only natural predator of all Green Lanterns".
Perhaps the ultimate example of this involving the actual Kryptonite was when Superman got exposed to some kryptonite from Jimmy Olsen's cracker box. Although in that instance, it was red kryptonite, so instead of weakening or killing Supes, it turned him into King Kong.
In the story 'Generations', set in a Pre-Crisis-ish world, we learn that there are tons of green kryptonite on Earth.
When Julius Schwartz took over editorship of the Superman titles in the early 1970s, he had a story where a nuclear accident converted all the kryptonite on Earth to iron. Then he had that balanced out by Superman dealing with a sand doppleganger that takes 2/3 of his power level and Superman ultimately decides to leave it at that. Unfortunately, readers didn't take to this revision and Schwartz was forced to backtrack.
In the early years following Superman's Post-Crisis reboot, Kryptonite was relatively rare in spite of the fact that Byrne had provided a more logical reason for its abundance (a chunk was lodged in Kal El's ship.) Instead, many villains could only get ahold of synthetic Kryptonite which lacked the punch of the real thing and wore out quickly. Of course, during this era Superman was powered down enough that many villains were a credible threat without it.
During The Death of Superman storyline, we find out that the bad guys made an engine that used Kryptonite. It's promptly used to try to kill Superman by attempting to bath him in its gas, literally draining the rock into non-existence.
Writers in later years have brought the situation back to pre-Crisis levels of inanity. The Superman/Batman story, K, has the duo cleaning up all the Kryptonite on Earth. By the end they've accumulated several thousand tons, and it is revealed Batman still has another half a ton or so hoarded up in his cave, 'just in case'.
One Silver Age story featured a single crime boss casually producing enough kryptonite to form a thick ring around the Earth. And that wasn't even his secret weapon.
An earlier story in that series featured a massive pure-Kryptonite asteroid hurtling towards the Earth which showered Kryptonite all over the planet when it was destroyed. (The sequel to that story arc explained that Supergirl's space craft was embedded inside the asteroid and was homing in on a signal from Kal-El's old space craft.) The size of the asteroid was never precisely determined but it was conservatively estimated to be the size of Brazil. Enough to account for the several thousand tons collected by Supes and Batman with enough margin for error for the writers to posit the existence of "hidden" caches if they ever feel like pulling out the Kryptonite card again.
The Silver AgeSuperboy comics featured a character, "The Kryptonite Kid, "who could generate and emit Kryptonite radiation. He made a few appearances in Superman comics as the adult "Kryptonite Man," including in Alan Moore's famous "Whatever Happened to the Man of Tomorrow?" story. He even gave rise to a trope of his own.
A very literal example. In one of the last Pre Crisis stories, Mr Mxyzptlk dumps Argo City (a huge chunk of Krypton) onto Metropolis. Tons of kryptonite were dumped all over town. Superman ended up leaving the planet. Thanks to the Crisis the storyline would never be resolved. On top of thatMxyzptlk got away scot free!
The New 52 brings back the idea that most Kryptonite on Earth is synthesized from the engine of Superman's ship.
Superman is also vulnerable to magic. While not technically a weakness, his powers offer no protection from magic itself whatsoever. A fire created by magic won't burn him any more than a regular fire of the same temperature, and a magic sword can only cut him if it could cut anything, but he can be mind controlled or turned into a frog just as easily as a human can. And in the DC Universe there is plenty of magic.
A number of stories pointed out that kryptonite isn't something humans should be casually playing around with or making false teeth out of either. It may not "take away their powers," but it's still radioactive.
Most notably Lex Luthor constantly wore a ring made out of kryptonite for years. This had the result of him eventually losing the hand, and later dying of cancer. He survived the death by transferring is mind into a clone body.
William Arcane in the New 52's edition of Swamp Thing can control all rotting matter. In one case, he killed a smoker with his own tar-stained lungs. Powerful guy, right? Kind of like Superman, his weakness is another green substance one can find nearly everywhere: chlorophyll, which Swamp Thing uses regularly. He's in a plastic bubble when he first appears.
Most of the heroes in The Belgariad are sorcerers of ridiculous power. But they can almost never use their power to solve their problems because they're always hiding from an army of magic-wielding mooks, who would sense any use of sorcery from a mile away.
In the Incarnations of Immortality novel "For the Love of Evil," the sorcerer Parry finds he cannot use his magic, because there is a sorcerer working for the group hunting him. Said sorcerer can detect his use of magic, and quickly find its location, from a long distance away. So, if he wants to stay hidden, he must not use magic.
An awful lot of the Big Bad villains whom John Taylor goes up against just happen to have the ability to shut down his Gift and/or block him from seeing anything useful with it.
In Larry Niven's "Man of Steel, Woman of Kleenex", he speculates on why so much darned Kryptonite has made its way to earth:
"For our purposes, all forms of kryptonite are available in unlimited quantities. It has been estimated, from the startling tonnage of kryptonite fallen to Earth since the explosion of Krypton, that the planet must have outweighed our entire solar system. Doubtless the "planet" Krypton was a cooling black dwarf star, one of a binary pair, the other member being a red giant."
(The surface gravity on such a world would be on the order of 100,000 G's, which would go a long way to explaining why Superman is so strong.)
Live Action TV
Happens to Hiro all the time in Season 3 of Heroes. You'd think that time travel, teleportation, and freezing time would make him almost invincible. Yet almost all his superpowered encounters are with people who can work around his abilities:
A speedster who's so good that time-stops merely slow her down to moving as fast as he does
We were reminded just how powerful Hiro could be without this trope holding him back, when he defeated Sylar and Ellein under ten seconds. All while he only had the mind of a ten year old, no less.
In Smallville, even though almost no one knows that meteorrocks remove Clark's powers and make him keel over in pain, a number of criminals just happen to have some meteor rocks around. It becomes a real surprise when Clark actually saving the day without any kryptonite hindrance. Cue several minutes of Clark trying to get rid of the kryptonite, followed by him trouncing the villain in 1/100 of a second.
Justified by the fact that in Smallville, Kryptonite is literally everywhere, with major mineral deposits from two different meteor showers. It's frequently depicted as a major environmental / public health hazard. The first meteor shower came along with Clark's ship (presumably dragged along in its wake), simultaneously explaining why no-one noticed an object from space impacting Earth.
Gets pretty ridiculous in later seasons though, when Clark's activities shift to Metropolis. In one example, Clark discovers the whereabouts of a non-powered serial killer who captures and quizzes soon to be married couples only to find that said villain, who has never met or heard of Clark, happens to have Kryptonite in his watch. It is never even mentioned until Clark shows up and it is never explained, nor does the villain ever become aware that the Kryptonite is hurting Clark. It is literally there solely to keep Clark from beating up the bad guy too soon. Amusingly, eventually Clark just headbutts the guy, sending him flying. As soon as he's far enough away, Clark busts his chains and rescues Lois.
In an alternate universe, literally everyone carries kryptonite with them to protect them fromUltraman, who killed Oliver for making this public knowledge.
Post-revival Doctor Who treats the Doctor's sonic screwdriver as a Magic Tool capable of, among other things, opening almost any lock. Not surprisingly, the Doctor often finds himself befuddled by doors with "deadlock seals" that the screwdriver is incapable of opening. Does not work on wood either, which is also everywhere, particularly in less advanced settings.
The revival of Knight Rider seems to take this tack, in that due to how incompetent most of the characters are other than KITT, the plot always seems contrived to happen in basements and otherwise deep inside buildings.
The vampires in Buffy and Angel seem to get into a lot of fist fights near wooden objects just waiting to splinter into stakes; furniture, crates, tree branches... a vampire can't fall down in that verse without getting impaled through the heart. It didn't help that vampires weren't exactly cautious of this weakness, one vampire attacked Buffy in a garden with a 2 foot high picket fence. The location of "the heart" is so generously (and inaccurately) applied it could well be considered a variation on the traditional trope overlapping with Artistic License - Biology. A vampire needs serious Plot Armor to survive a piece of wood puncturing any part of their upper torso.
This trope was used in every medium of Star Trek to avoid the plots falling apart under the weight of the franchise's accumulated Phlebotinium. You can be guaranteed that any episode based around a problem that could be solved in seconds with the use of the transporter, the tractor beam or the ship's sensors will be drawn out because the appropriate equipment is mysteriously not functioning or out of range. Of course, the show would have been awfully boring if they had a commonplace solution for every scenario.
In Star Trek: The Next Generation they also periodically tried to rationalize away why Troi did not sense things that other episodes implied she should have been able to. Often species were selectively immune to Betazoid telepathic powers whenever it was necessary to the plot. This was especially interesting because this usually applied to mostly humanoid aliens in mystery type episodes, yet Troi could often easily sense even very strange Energy Beings at other times. She was also made only half-Betazoid to rationalize a scaling-down of her powers.
Parodied in the Superdude sketch on All That. The eponymous character had many amazing powers and his only weakness was being lactose intolerant. Of course, every villain he fought except one was dairy themed (examples include Milk Man, Butter Boy and the Dairy Godfather). Fortunately for that villain, the Evil Superdude, milk was used anyway when confused bystanders had to Spot the Imposter.
Sportacus in LazyTown has a BIG weakness: SUPER HIGH CALORIE SUGAR.
In The Big Bang Theory, Leonard Hofstadter takes a deep, deep, breath and covertly gives Penny the weapon that will defeat Sheldon Cooper. He warns her to use it well and wisely and even describes it as "Sheldon's Kryptonite". (It's his mother's address and phone number).
In many roleplaying games, this trope can haunt a GM. Magic is often supposed to be rare, yet few PC groups abstain from taking a wizard along. When a game system then posits that magic can only be effectively countered with magic, the GM is hard-pressed to explain why the opponents of the day do in fact have access to their own spellcaster or magic items unless he wants the magically boosted party to plow through their enemies effortlessly.
This is also the reason most systems are rather stingy with handing out powers that fundamentally change core aspects of the system, like immunity to common damage types or flight.
You can almost feel the frustration with this in the Iron Heroes d20 setting, which allows the GM to grant whatever kind of magic he wishes to NPCs but restricts players to a very restrictive, skill-based, horror-themed form of magic almost entirely to prevent them from easily coming up with the convenient counter to whatever the villain is up to.
Many role-playing games, particularly super-hero related, provide bonuses (feats) if penalties are taken elsewhere (flaws), leading to min/maxers to take tremendous powers in exchange for crippling weakness... to something so mind-boggingly rare that it should never, ever show up under normal circumstances; like Super-Deadly-Ultra-Sensitivity to the pollen of a rare flower that blooms once every 20 years at the top of Mount Kilamanjaro... so what does the GM do? He makes the primary villain THE KILAMANJARO PLANT-MAN, an international crime lord capable of creating blooms of any plant that grows, has grown or will grow on Mt. Kilamanjaro... indeed...
A lot of these games do note that Game Masters should veto anything too obscure, and a lot of systems give a bigger reward if the substance is more common. For example in the Hero System vulnerability to a rare space rock would probably be worth a +0 bonus (meaning you'd only get points for intensity), while something more common like silver would be worth five or ten extra character points before deciding on intensity.
The Epic Archetypes from City of Heroes, Peacebringer and Warshade, are very powerful and versatile but are vulnerable to quantum array weapons, which mooks have much more often when one of them is present on the map.
Or if they're especially unlucky they'll meet a Void Hunter, who is also resistant to their attacks. And if they're part of a large team, Nictus start showing up...
To this day, Peacebringers and Warshades are only begrudgingly accepted by some of the more serious Super Groups, if not outright shunned, for that very reason; some story arcs and Task Forces are hard enough without suddenly having to deal with an infinite spawn of grossly overpowered Nicti. Conversly, however, the Villain archetypes are not only far more customizable and powerful, they carry no downside whatsoever. Well, except that you had to level up one character to 50 in the largely depopulated and difficult-to-navigate Rogue Isles, then level up the Epic in the same area... At least until Going Rogue came out, streamlining the travel process and opening up Epics when you got a character to twenty, often considered the point at which the game makes you start actively trying.
The world seems to be going out of its way to give Shiki more and more impossible to kill enemies after Tsukihime'. First, we have Kagetsu Tohya, which had a rather bizarre set of circumstances around it preventing Shiki from killing the source. The best one was that he simply didn't want to. Melty Blood introduces a vampire turned phenomenon with Wallachia, who can't die under normal circumstances. The Dead Apostles listed also has several suspiciously worded entries for enemies that Shiki can't simply oneshot, such as Type Mercury.
Type-Mercury is an outlier, even among the Dead Apostles. ORT belongs to a completely different order of beings, all of whom lack concepts of death.
In Fairy Wars Cirno's schtick is freezing bullets. She can't freeze fire bullets or lasers. While lasers remain thankfully rare, once you hit Stage 2, fire bullets are all over the place.
In the video game of The Darkness, your weakness is any strong light, which nullifies your powers. Flashbangs are at one point utilized against Jackie, which takes him out.
In Star Wars: Knights of the Old Republic, every damn metal sword is enhanced with cortosis so that the game doesn't have to deal with the fact that lightsabers would cut through anything else (when the swordfighting animations clearly show the characters blocking and locking blades regardless of what they are made of).
Even (apparently) the gaffi sticks of the primitive Sand People.
Every sword you run into being made with cortosis is justified if one assumes that lightsaber-armed opponents are fairly common. A sword made of anything else would be potentially useless. As for the gaffi sticks... don't think too hard about that.
A particularly extreme example was in Generation IV, which brought in Stealth Rock, which set a trap that would strike any Pokémon switched in by the opponent for a fixed portion of their health, regardless of their defenses or the attacking ability of the Pokémon that set it, based on their vulnerability to Rock-type attacks, from a mere 3% to a full half of their health bar. Since it was a widely-useable TM, Stealth Rock could, and would, be found on a wide variety of Pokémon, and setting up Stealth Rock was generally considered first priority in most Pokémon battles; also, the only way to remove it was by using the move Rapid Spin, which was found on a much narrower selection of Pokémon, which would likely be placed on a team specifically for that use. In short, it was absurdly easy to put up, and just as absurdly difficult to get rid of. Basically, Fire, Ice, Flying, and/or Bug Pokémon that didn't have a second type that mitigated their Rock weakness (and especially Pokémon that possessed two of those types) were all rendered effectively useless in the metagame just because this trope hit them that badly.
Grass-types get hit by this trope really hard. They are meant to counter Water-types. However, the vast majority of Water-types learn the move Ice Beam, a hard hitting and reliable move that hits Grass super effectively. So, it is a rock that is hit hard by both paper AND scissors.
Five Grass-Type Pokémon are given the shortest end of the stick possible: Exeggcute, Exeggutor, Celebi, Snover, and Abomasnow. The type combinations of these five Pokémon (Grass/Psychic for the first three, Grass/Ice for the last two) give them all seven weaknesses, the largest amount of weaknesses on any Pokémon in the whole game (Snover and Abomasnow's second type even elevates their weakness to Fire to a double weakness).
The infamous Superman 64 has "Kryptonite fog" in every level, diminishing his superpowers. Of course, it's just an in-game explanation for the severe distance fog that was supposed to mask the Nintendo 64's poor draw distance.
The Metroid Prime series introduces Phazon, a radioactive substance that also has great potential as a energy source/weapon. In the first one, it's on one planet, carried there by a meteor. The second game reveals an additional planet was also struck by the same kind of meteor, and now has Phazon on it as well. By the time the third one rolls around, another three planets have been struck by these meteors and the game starts with you trying to prevent one from striking a fourth planet. Phazon is now widespread enough for both the Space Pirates and the Galactic Federation to use it as weapons. Justified in that these meteors are revealed to have been launched from a sentient living planet made of Phazon. It is trying to get everywhere.
Bass lampshades this trope in Captain SNES, telling Vegeta that he isn't contacting Superman because he's pretty sure the god-level entity tearing up Nexus has magic powers, and even if he didn't Kryptonite is so common that the ice cream vendor they're meeting in front of probably has Kryptonite-flavoured ice cream. He in fact has two kinds.
Superman, after being hit with Kryptonite yet again: Kryptonite! Where do you keep getting this stuff?!
Whateley Universe: Fey is allergic to cold iron and synthetics; yes, she can be given a nasty rash by your spandex costume. Blacklight is weak to bright light. And Fractious has OCD and Generalized Anxiety Disorder, so she can be stopped by dirt, dust, pollen, mud...
Kinda-sorta justified in Superman: The Animated Series. Superman's ship used a Wormhole drive: When it was sent to Earth a lot of Kryptonite got caught in the wormhole radius and went along for the ride. And it doesn't show up everywhere. Once Luthor realized Superman was vulnerable to Kryptonite, he spent time offscreen stockpiling every little bit he could get his hands on, to the point where he pretty much owns all the Kryptonite on Earth except for that huge rock in Skartaris. He's one of the only villains in the series that regularly uses Kryptonite against Supes which bites him in the ass when he gets cancer like his counterpart in the comics; the others that use Kryptonite like Metallo got it from Luthor.
Batman has a piece in a lead-lined pouch in his utility belt just in case Supes goes rogue, presumably swiped from the chunk the Joker managed to get his hand on during Bats and Supes first in-universe meeting.
In the 1990's X-Men series, the X-Men and several other characters with powers had to fight an alien creature in the subway tunnels under New York. Things were going pretty badly until the thing hit the third rail... of course, Storm was nowhere to be found in that episode. A rather egregious omission since the creature went after the Morlocks first and Storm was their honorary leader. Well she is claustrophobic.
Also lampshaded in Batman: The Brave and the Bold episode "Triumvirate of Terror"; when Luthor says "You've ruined my plans! But I can still ruin YOU!", Superman responds (in a very bored and/or tired tone of voice) "Here it comes...", just before Luthor pulls out a hunk of Green K. Then when Lex throws the rock, Supes calmly picks up a manhole cover, deflects it into the sewer, and covers it up.
Similarly, "The Super-Batman of Planet X!" had Batman develop Superman-like powers while visiting an alien planet; however, the resident Luthor Expy discovers that quartz, a ludicrously common mineral, has the same effect on Batman that Kryptonite does on Supes.
Played with in Megamind. Metro Man's weakness to copper would render him vulnerable to this trope...if he hadn't made it up to fake his death.
A variant can be found in Beast Wars, where the robots need energon to survive, but if they're exposed to too much raw energon, they'll overload, hence why they need the beast alternate forms. Apparently, some aliens decided to seed the entire planet they crashed on with a crapload of energon, so the entire planet is unsafe to them for prolonged exposure.