Mobile Suit Gundam 00 has the mysterious GN Particles, which can jam communications, be used as a propellant, be used as protective shielding, and is even the basis for the Gundams' energy swords. GN Particles have the added bonus of coming in two distinct "flavours"; the "Pure", green coloured particles used by the protagonists, and "Impure", red (or orange, in the second series) particles used by the villains in their mass-manufactured drives. Incidentally, the red particles seem to impede cell functions and healing in humans, while the green version improves it.
Devil Fruit. Eating one can give you any superpower imaginable, the type depending on the fruit you ate. Powers range from animal transformation to elemental control to coming back from the dead as a living skeleton, among a lot of other effects. What really pushes it into Green Rocks territory is the ability for inanimate objects to "eat" the animal-type fruits, becoming Empathic Weapons in the process. But, unlike some Green Rocks, the Devil Fruits have a strong stigma. The user is unable to swim, and loses all power upon significant contact with seawater. In addition, the result of eating the fruit is generally unknown. You could control lightning, or you could gain a completely (or seemingly) useless ability. There is no antidote, and eating a second fruit causes instant death.
Devil Fruit powers seem to encompass any sort of power you can think of, and more. However this means that they also encompass the sucky ones. Namely there's a fruit that allows you to change into each type of animal (ranging from specific species to a general family). However, this means that if an animal ate a fruit that turned them into their own species, it effectively robbed them the ability to swim, while giving them nothing. Again, there's no way of knowing this beforehand. Word of God stated that if a human ate the Human-Human Fruit, they would simply be "enlightened", but didn't elaborate on what this meant or if animals had the same effect. Good thing only one fruit of each kind exists, and the regular human one was eaten by a reindeer.
The Dials, magical seashells from the sky (somewhat vaguely implied to be related to the Den Den Mushi) that all have different magical powers based on color, fit the trope much more. Much of the Skypeia arc was the Skypieans getting New Powers as the Plot Demands attributed to Dials and the Dials are used from then on in the story to explain away the setting's Schizo Tech.
In weaving together Space Fortress Macross, Southern Cross, and Genesis Climber MOSPEADA into one long story arc, Robotech, Harmony Gold introduced "Protoculture" which was a mysterious energy source that allowed the creation of transformable mecha, and is also (at least in the Mospeada part of the story) the fuel used to power them, while in the first part, the humans barely seem to understand what it is.
Yuusha-Oh GaoGaiGar has a literal green rock, the G-Stone, used as the power source for all of its main mecha, as its power output increases as a function of the pilot's or robot's raw courage. There's also a red counterpart, the J-Jewel, with even less well-defined powers, one of which is explosive output when combined with a G-Stone. Indeed, many of the fuzzy properties of the G-Stone and J-Jewel are related to their interactions with other substances and energies. Finally, there's Zonder Metal. Just... Zonder Metal.
The Silver Crystal from Sailor Moon seems to gain whatever properties are necessary for a particular arc's plot. It can defeat evil beings, except for when it only seals them away or heals them! It can grant its user's dying wish, except when using it doesn't cause death! It's useful for saving cities of the future, initiating Transformation Sequences, and also apparently could serve as a great power battery for Big Bads! It even plays music!
Code Geass has a couple of examples. One is Sakuradite, a natural resource with high conductivity that's used in everything in the series; the Lancelot's Super Prototype-ness is explained by saying that it uses more Sakuradite than normal KnightmareFrames, giving it incredible energy efficiency. A better example is the Gefjun Disturber, a device that blocks Sakuradite's conductivity, making it work something like an EMP weapon. It also somehow has the properties to block radar and aids in the blooming of energy weapons, which allows the Gawain's hadron cannons to go from awful to amazing.
Which was inspired by Getter Rays from Getter Robo. Practically the same thing, actually (which is lampshaded in Super Robot Wars Z2), including leading to the destruction of the entire universe if over/misused.
Legion in the manga version of Chrono Crusade is a strange version of this trope. It's described as the "building block" of a demon's body, similar to human cells, and it's what fuels their regeneration abilities and probably aids a demon with their unique powers as well. On top of that, it's also used to bring a human girl back from the dead (and give her regeneration powers), possibly turns a human boy insane by connecting to his mind, and dissolves another human being on contact, apparently eating him alive. And to top it all, legion also seems to be the building blocks for demonic architecture as well, which allows them to create shields and hidden doors, among other things. When left unchecked, it can cause a host to turn into a spiky mutant with a mind driven so insane it's boiled down to its basic instincts of kill or be killed. Scary stuff.
Lacrima Crystals in Fairy Tail tend to have whatever power is convenient at the time. Lightening Storms, engines, dragon slayer magic.
In the original Superman comics, Red Kryptonite had a random yet temporary effect. And guess what Pink Kryptonite causes?
In the Incredible Hulk comic books, gamma radiation often has a completely random effect on the individual exposed, usually something to do with their psychological makeup, although this effect is often completely arbitrary. This is the way they explained gamma radiation turning Hulk into a id-like monster, She-Hulk into a fun-loving Amazon, Doc Samson into a musclebound superhero type, and the Abomination into what you'd expect.
It's also been revealed that most people would just die horribly when exposed to such large amounts of gamma radiation (which is a rather more plausible result), and the people who got superpowers from it did so because the radiation interacted in some pseudoscientific way with random genetic anomalies they already had. It was explained once that everyone who got a positive mutation from gamma exposure had a single common genetic ancestor somewhere back in the mists of history. No one else has that funny genetic quirk. This was demonstrated when the Leader dropped a gamma bomb on a town of about ten thousand people or so; everyone died, except five individuals who mutated. One of the Leader's main goals is perfecting gene therapy to allow anyone to achieve powers from gamma radiation.
The Terrigen Mists, the source of superpowers for Marvel Comics' The Inhumans, bestow random superpowers and physical mutations upon anyone exposed to them. However, if any non-Inhuman is exposed to them it will inevitably lead to a serious Deadly Upgrade or some similarly unpleasant fate.
In the Just Imagine... line of comics where Stan Lee re-imagines several classic DC characters, almost every character with powers gains them through some form of green energy, mist, or chemical. The green manifestations turn out to be linked back to an ancient magical tree that may be Yggdrasil or the Tree of Knowledge.
The Top 10 universe has S.T.O.R.M.S. (Sexually Transmitted Organic Rapid Mutation Syndrome), a sexually transmitted disease that can mutate you into a monster, a god or (most often) a monstrous corpse.
Marvel's mutant gene is probably the most extreme example of this, letting writers forgo the need for any sort of origin story what so ever by saying the character's a mutant. Mutants can have any power imaginable, ranging from the ability to regenerate any and all wounds received, to duplication. Whether this was a bad thing is debatable, since non-mutants' origin stories are often cheesy or downright stupid.
Scarlet Witch's mutant power over probability is another example, letting her do anything the writers need, like making all the bullets in a gun defective. Some Willing Suspension of Disbelief is needed, since she's been known to use her powers to do things physically impossible no matter how much luck you have, like make gravity stop affecting her. Later retconning revealed that her powers were combined with actual magic to far exceed what should have been possible. Yet later there were again retconned as the power to play merry havoc with the very fabric of reality as she pleased. Wanda's powers were also affected by her having been born on Mount Wundagore, a mountain where a Chthon, an Eldritch Abomination, was imprisoned.
The exact same burst of radiation gave four people each a completely different power in Fantastic Four. Some iterations have explained it as the powers coming from what each felt was their greatest weakness. Which just happened to correspond with the classic Alchemical "Elements": Air (Invisible Girl), Earth (The Thing), Fire (The Human Torch) and Water (Mr. Fantastic). Or possibly the four stages of matter (gaseous, solid, plasma, & liquid, respective to the previous examples), if you prefer a more scientific outlook. The current explanation is that Reed was partially responsible for designing the entire universe.
In Milestone Comics' Dakota Universe, most super powers are the result of exposure to Quantum Juice, a.k.a. Q-Juice.
Multiple powered characters in DC Comics are a result not from the accidents they had, but mutating to survive the accidents. As seen in the Hitman series (and in other comics), it's fairly common for people to crawl out of a vat of toxic goo and go on a rampage. The title character is often called in to provide a very discreet bullet.
Reed Richards (Mr. Fantastic), Tony Stark (Iron Man), and Stephen Strange (Doctor Strange) are Marvel's walking green rocks. It just depends on whether you need something involving physics or biology, technology and computers, or magic!, respectively. That is, when they decide to get off their asses. Reed isn't a trope namer for nothing...
Supreme has supremium, an obvious homage to kryptonite. Its radiation alters reality depending on its constantly shifting color, both giving the title character his powers and weakening him, sending people through time, and turning a man into a growing mess of arms and legs.
Vandal Savage gained immortality when, as a caveman, he slept near a mysterious glowing meteorite on a cold winter night for warmth. Said immortality isn't quite perfect. Savage needs to eat the flesh and organs of his own descendants to maintain his longevity. The same meteorite gave The Immortal Man his powers, which work differently than Savage's; instead of living forever he is continuously reborn into a new life as soon as he dies.
Towards the end of its run, Tales of the Unexpected introduced a floating little plot device called the Green Glob. It would enter a person or object and do whatever was needed to teach the main character(s) whichever particular Aesop they were in need of learning.
Spoofed in Atomic Robo with crystals. They can do everything! - at least according to Dr. Dinosaur. Robo himself is quite doubtful of this claim.
Films — Animation
Heavy Metal: The Loc-Nar is a Green Rock; a floating, sentient, utterly evil, sadistic Green Rock. It's a green sphere that proclaims itself (correctly, given the havoc that constantly tends to surround it) the sum of all evil in Heavy Metal's universe, and is the MacGuffin for all the stories told in the movie.
In Monsters vs. Aliens, Susan gets hit with a huge, glowing, green meteorite. It's "quantonium", the phlebotinum of the plot. It turns her into a (nearly) fifty foot woman and leads the Big Bad right to Earth.
Films — Live-Action
In District 9, the "black fluid" serves as some sort of fuel for a space ship. It has the bizarre side-effect of altering the DNA of any human exposed to it, causing them to transform into a "prawn".
My Super Ex-Girlfriend: The title superheroine got her powers from a magical meteorite. In addition to making her a Flying Brick, it also turns blondes into redheads and redheads into blondes. It can also take away her power if she comes in contact with it a second time.
One of the finest examples is in the Dune series of books. Melange, a.k.a. "the Spice", was a combination of MacGuffin and Applied Phlebotinum. It was a flavoring, a drug, a source of magical visions, and it gave you cool-looking blue-on-blue eyes. It also made Faster-Than-Light Travel possible, and acted as a mutagen on consecutive generations of users. It also quadrupled the lifespan of anyone who took it. Too bad that The Spice was also insanely addictive, had only one source, and being cut off from supply resulted in an agonizing death.
As elaborated in some of the later books (including later books by the author's estate) the Spice allows fast space travel because it confers a certain degree of prescience/psychic-knowledge to the navigators of the ships, which would otherwise be impossible to safely navigate, at least not without proscribed A.I. intelligences. The actual FTL physics are separate from the drug's effects.
In Frank Herbert's books the Spice only had two properties — life extension and consciousness expansion. Essentially the ultimate nootropic. The variation of effect was due to the variation of short and long-term dosage. At low doses, it merely prolonged life and granted a moderate enhancement to thought processes. It was only at very high doses that the mind was sufficiently enhanced to manifest prescience; and for the addiction and fatal withdrawal symptoms to be an issue (and for the blue-within-blue eyes side effect to show up). FTL travel was stated to be purely technological in nature, and implied to be related to the Holtzman Effect. The prescience and cognitive enhancement granted by the Spice was necessary for navigation through folded space, since electronic A.I. has been subject to both legal and religious prohibition since the Butlerian Jihad (although the world of Ix is implied to have developed some in secret).
The first book makes it abundantly clear that it can be used as, well, a spice. It tastes and smells like cinnamon. Though some characters state that it is never quite the same. Another properties is that the Spice is also stated to act as a neutralizer for most basic poisons in the Duniverse. It's also used to make cloth, plastics, liquor, candies, and many other things. Is there anything the Spice can't do?
The gelstei crystals in the Ea Cycle come in all the colours of the rainbow and then some. Each type has different powers, but the more powerful ones are versatile. For example, green gelstei can be used to both heal and create mutated monsters.
Keys to the Kingdom has the Keys, the description of which IS "magical items that can do almost anything". Although they might have specialties, seeing as the Third Key is almost always shown manipulating water, while the Fifth Key can transport its user anywhere they've already been, so long as there's a reflective surface there. And the Second Key is specifically used for making things, the Sixth Key appears to enhance spells written with it, as it is a quill pen and House sorcery almost always involves writing, and the Fourth Key seems to be awfully useful in a fight... Which may indicate that the Keys have powers specific to the demesne they preside over.
In The Lorax, the Once-ler uses the tufts from the Lorax's truffula trees to make an all-purpose consumer product known as they need.
It's a shirt, it's a sock, it's a glove, it's a hat And it has other uses, far beyond that
Downplayed in the Destroyermen novels. Polta fruit is starting to seem like this, though none of its so-far-established properties are really thoroughly outlandish. You can eat it straight, and you can mash it up and ferment it into seep, the Lemurians' ethyl alcohol delivery mechanism of choice. The pulp left over from fermentation is used in wound treatment as an antiseptic and topical anesthetic, and in later books they discover that partially fermented seep has properties similar to battery acid, enabling construction of portable power sources.
The Trope Namer is Smallville's kryptonite. It has been used to kill people, heal people, give people powers (the powers can be anything, including, cold, fire, shapeshifting, electricity, intangibility, bee control, death touch, splitting, sonic scream, and more... or in short, with no common theme), erase memories, used as car fuel, add strength to dynamite, give back memories, make chewing gum, make Clark Kent crawl on the floor in pain, make Clark Kent act like a dick (red), make Clark Kent lose all his power (blue), make Bizarro Kent explode with too much power (blue), split Clark Kent into a Literal Split Personality and inexplicably fuse them back (black), make Clark Kent crazily paranoid (silver), make a phone call to twenty-four hours ago (by teaming up with Lightning Can Do Anything), cause two people who were nearby during an explosion to psychically bond, make counterfeit banknotes, etc., etc. And it GLOWS! And even here, it is... diverse. Sometime it glows, sometime it doesn't, sometimes it glows only in Clark's presence, sometime it always glows, and sometimes it could somehow dim the lights around it by being next to Clark.
Star Trek: Voyager. Seven of Nine's Borg implants and nanoprobes were used to resolve a number of problems.
The almighty Deflector Array in Star Trek. Any time anything in the universe that's even remotely energy-based needs to be absorbed, converted, transmitted, created, destroyed, or, well, deflected, you can count on the ship's engineer thinking up a solution that uses the deflector array. No ship should be built without it! Federation/Starfleet ships seem to be the only ones in the Trekverse to have an obvious main deflector dish (and not all the time). Everyone else, from the Klingons to the Romulans to the Cardassians to Voyager's Delta-Quadrant-Menace-Of-The-Week, seems to get by without them. Which is especially odd given that the basic vanilla function of a deflector array is to function as a futuristic cow catcher and would be hugely important if you didn't want to destroy your ship by flying into a piece of grit at warp speed...
Naquada is practically indestructible, is a room-temperature superconductor, enables forming stable wormholes, is a source of power second only to zero point energy, explodes with super-nuclear force on contact with potassium, increases the power of existing nuclear weapons, has an easily detectable energy pattern, etc.
Naquadria is exactly the same, except more powerful, highly radioactive, and with a tendency to explode. Whether the people using the stuff want it to or not. Plus that slight problem with creating stable hyperspace windows with it. In Stargate Universe, Naquadria is responsible from blowing up two planets.
Promicin, the luminous green neurotransmitter from The 4400, has extremely unpredictable effects. Anybody injected with it will develop some kind of superpower, but there is apparently no way to predict what power that will be. It also has a good chance of killing you but that's the price of power, even if it does suck. It also has the power to ignore the blood-brain barrier.
On Land of the Lost, the light crystals could do any number of things, by themselves or in combination with other colors, including emit light, heat, and energy, explode, and open dimensional portals.
Kind of a literal example, but in one episode of Blackadder, Baldrick and Percy attempt to turn lead into gold. What they end up with instead is a glowing green rock that can only be described as "green".
The British sci-fi drama Misfits: In just six episode the storm that strikes in the first episode has given time travel, mind reading, mind control, invisibility, psychopathy, the ability to make others hair fall out, immortality, youth, and probably a few more!
Monty Python's Flying Circus: String can be used to tie up small parcels, attach notes to pigeon's legs, destroy household pests, prevent floods...
In Warhammer lore, Warpstone is a magic rock, a form of solid Chaos, that absorbs all light from the surrounding area while emitting its own green light. It can be used to power magical machines or for Faster-Than-Light Travel or as a magic looking glass or to create mutations, etc. Generally, though, it's The Corruption. Oh, and did we mention that one of the two moons is made out of this stuff?
In Warhammer 40,000, you get all sorts of magic rocks-Necrodermis, Standard Template Constructs, wraithbone, and the Warp itself all function as magic rocks at various points. Wraithbone is more or less the same as Warpstone, as it is solidified psychic energy. However it is far less chaotic than its fantasy counterpart, but apparently forms almost everything the Eldar uses, down to possibly their clothes.
Shadowrun: "Nerps for acne. Nerps for boredom. Nerps for kidney failure. Nerps for energy. Nerps for ring-around-the-collar."
Large regions of the Red SteelD&D setting are contaminated with a reddish toxic mineral called cinnabryl, which impairs mental attributes in those who are exposed to it. However, certain cinnabryl-derivatives can not only offset this effect, but can confer a wide range of superpower-like abilities to those who know how to prepare and administer them. Just to cap it off, depleted cinnabryl can be refined into a superior grade of red-tinted steel (hence the name), and smokepowder for firearms can be crafted using its residues.
Tiberium from the Command & Conquer series is the most valuable substance in the world (leading to the GDI and Nod fighting over it) and will either kill or mutate anybody who steps in it. It also corrupts the land so much in the sequels that by the second game's expansion, the Earth's air and atmosphere is one year or so away from become toxic to humans. To top it off, it's part of an alien invasion plan. It's green. There's also a blue variety, which has aged considerably, and thus is much more valuable, but tends to... react, when people start slinging explosives around. There's supposedly red too... To be fair, Tiberium (at least the CNC 1-2 variety) contains valuable metals in high yields, conveniently sent to the surface in packed crystals. In CNC3, its more unappealing properties come through radiation. Either way, its extremely toxic, and in Tib Dawn/Sun's case, mutagenic.
Tiberium is also essential to the Scrin life cycle. The species is entirely dependent on it for its survival, and their modus operandi seems to be seeding a planet with a Tiberium meteor (or waiting for it to be seeded), and then biding their time until the population destroys itself fighting over the new resource or over unaffected territories. In the end, the crystal itself makes life on the planet impossible, and eventually grows into the planet's crust and hits the mantle, triggering an enormous explosion that signals the Scrin fleets to move in.
The official strategy guide for Dawn explained how Tiberium allowed several for several of the aversions of reality seen in the game, like aspects of Easy Logistics (on-field construction) and Ridiculously Fast Construction (very effective on-field construction). Thus, Tiberian War: the value of Tiberium is both a reason for war and a necessary element of the modern way of waging war.
Tiberium makes an appearance in the Sims 3 as an easteregg, it's attributes are that it can cut itself into a unique shape from it's raw form (all other gem types in this game must be cut by the player), it's ridiculously valuable and makes a Sim ill when carrying it. Rumours of Tiberium being able to spread itself if left on the ground as in it's parent games are untrue though.
Phazon from the Metroid Prime series was a poison, a weapon, and fuel, and interestingly, was the only thing that could hurt the Metroid Prime despite it also causing the metroid's transformation in the first place. In Corruption it turned out to be the corrupting influence of a living planet of the stuff seeking to take over the universe. Whoa. Oh, and did we mention that it's sentient in all of its forms?
Curiously, Phazon has No Ontological Inertia, the destruction of the planet Phaaze, the source of all Phazon leads to the obliteration of all Phazon everywhere even from the planets and life forms it was infecting.
Skies of Arcadia features a system of six Green Rocks of which only one is green; the others are red, yellow, blue, purple, and silver. These rocks are energized meteorites that fall from the moons and are used as a Magitek-ish power source for practically every vaguely mechanical item in the game, including prototype airship cannons, vehicle engines, torches, stoves, and liquor distillers (silver makes the good stuff). Said rocks also allow their owners to cast magic spells, or physically attack with elemental power by slotting a rock into their weapon.
The Chaos Emeralds from the Sonic the Hedgehog series, whose functions throughout the games include everything from heroic transformation to manipulating time to powering doomsday machines.
The Fire Emblem in the series by the same name seems to function somewhat like this. In Sacred Stones it's a plot device, and in Shadow Dragon all it does is let you open locked doors and chests without a key.
The psychic summer camp in Psychonauts is built over a large deposit of Psitanium, which enhances psychic powers of the strong-minded and causes insanity in the weak-minded. Carrying a large block of this allows Cruller to come to the rescue without splitting into his multiple personalities.
The Jak and Daxter series has Eco, a substance that comes in various states and colors: Green (healing), Red (strength), Blue (speed/motion), Yellow (ballistics), Dark (toxic), and Light.
The Dig featured glowing Life Crystals created by an advanced alien civilization, which are capable of bringing the dead back to life (albeit with resulting insanity and crystal-addiction). You can probably guess what colour they were. For some reason, the crystals were also used to power the various alien machines found throughout the city.
Psynergy Stones in Golden Sun, which were spread over the world by the erupting Mt. Aleph, hit animals and turned them into monsters. They had different effects on more sentient beings (humans, talking trees...), as well as the landscape (caused the sudden apparition of a forest, and a swamp in the second game) and non-living things such as statues. Everything that hinders you but isn't directly tied to the plot is blamed on them. To Adepts, they restored their Psynergy. They were purple and sparkly, though.
In Half-Life, green (actually gold) rocks and the mishandling of said rocks caused the resonance cascade, which allowed the creatures from Xen to come a-swarming in and nearly end humanity as we know it. The Nihilanth kept three of these crystals in its chamber to heal itself.
In Half-Life 2 : Episode 2 it turns out that someone arranged for the rock to be placed into the machine for exactly that purpose, and that the computer problems on the same day were most likely to cover up that the machine had been tampered with. It is confirmed that the G-Man procured the crystal which blew up in the test chamber but for who's request is unknown (seeing that he presents himself as a freelance contractor, probably the Combine hired him). They also power that nifty Gravity Gun.
Myst IV has actual green rocks on the prison Age of Spire. This mineral allows rocks infused with it to hover in repulsion to the sun-like core of the age. It also comes in crystals which store some kind of negative static electricity, and any grounding makes it discharge. Sirrus put this to use to power his machines and create sonic explosives.
In Final Fantasy XII, Magicite is merely a stone that has absorbed enough Mist to become magical itself, allowing one to cast basic elemental magic, keep airships aloft, or create city-wide barriers. The most significant (and powerful) Magicite in the Ivalice Alliance world is known as Nethicite and Auracite.
Energy X serves this purpose in Freedom Force and its sequel. Not only does it give almost all the super-characters their powers, which are as varied as anything the X-gene ever provided, but it provides the power-ups that are sprinkled around each battlefield. It heals injuries, temporarily super-energises characters, provides permanent power boosts for characters and can give the team a bonus helping them to recruit more members. And it comes in easy-to-carry canisters! And turns out to be a sentient energy being with dark designs on the universe! Too bad the third in the series was never made...
Ember from Torchlight. The game takes place next to a mine for it.
In Alpha Prime, hubbardium are literal green rocks (Turned that way due to radiation from Glomar's heart) that are implied to have a variety of uses ranging from powering things, to alcohol, to Bullet Time.
The Harvest Moon series' equivalent to materia — Wonderfuls. Seven different colors with seven different effects (Blue and red ones extend the range of your tools, green ones reduce the amount of stamina needed to use them) with some varying slightly depending on which tool you put them in (Orange Wonderfuls increase the amount of water your watering can holds, and acts as a yield multiplier in your other tools)
One of Singularity's writers is quoted as saying that E99 can do whatever the plot needs it to. This includes time travel, gravity manipulation and time manipulation for a start.
Team Fortress 2 has Australium, a mineral branded with the image of a man boxing a kangaroo that's responsible for the Australians' hyper-advanced technology and causes literal Testosterone Poisoning. The Engineer's grandfather Radigan Conagher was given 100 pounds of the stuff which he used to build all sorts of inventions, but the radiation eventually mutated him into a shirtless Australian with chest hair in the shape of Texas.
Valkyria Chronicles has ragnite, a mysterious glowing substance used in anything humanly possible from first-aid kits to ammunition, including, but not limited to, street lamps and engine fuel and laser weapons.
The runes in Runescape could count. While the player can only use the spells of whichever spellbook they're currently using, several other characters have been using them for spells that you can't use. For instance, a child in the "Meeting History" quest was shown banging together runes (an air rune and a fire rune, if memory serves correctly), which caused a small explosion. Nothing big, harmful, or destructive. Just enough to make a few sparks to start a fire and make a loud noise.
Lyrium, a mineral that absorbs and stores magical energies from the surrounding environment. In mineral form it is a blueish green, becomes purple when crushed, red when ground to powder, and finally blue when turned into potions. The most common and direct use is in mana potions, but it is also used to forge magic weapons, destroy a persons magical abilities (and part of their minds), make warriors resistant to magic (and addicted to the stuff), and part of the concoction that turns normal people into Grey Wardens without mutating them into monsters. Whenever you want to create something magical, there surely is a lot of lyrium involved in the construction.
It is also alive on some level, and dwarf miners find veins by listening for want is always called it's "song", new veins can be seen growing in old ruins, and prolonged exposure causes anything from idiot savant status to full-on insanity. Hawke and company find large amounts of a new and unexplained red type in a long-lost Dwarven city which had a number of unique properties they never found any answers to. Whether any of this has any connection to the Dwarven religious belief that the dead "return to the stone" or the rise of the Darkspawn is unclear, but there is definitely more to it than has been revealed so far.
There are also lifestones, a rare rock that has existed in close proximity to lyrium ore, and as such, they have absorbed some of its traits. Crushing a lifestone gives the user a small bonus to nature resistance for a short time — reasonable enough. But in addition, lifestones enhance the natural properties of other materials used in item creation, and how! These magic rocks are used as natural property 'enhancers' in all sorts of antidotes, salves, poisons, and grease traps conveniently making things more healing, more deadly, more acidic, or more greasy just by mere presence, it seems.
Humans in Mass Effect first developed psychic powers when a fright transport of Element Zero exploded during reentry over Singapore. While no immediate health effects were noticed, traces of the substance inhaled by pregnant women affected their unborn children which developed biotic potential, though they still require implants to amplify their powers for combat use.
Mass Effect 3 suggests that this might probably also be the source for the apparent natural bionic powers of Asari Who secretly had access to a complete and working database of Prothean technology and would have had thousands of years to permanently modify the DNA of their entire species.
Element Zero could well be a Trope Codifier. It (and the eponymous "mass effects" it creates) are responsible for and a key component of just about every major technological development in the games.
The Blacklight virus in Prototype is defined to be the answer to everything in biology.
Imulsion in Gears of War was originally discovered as an incredible fuel. It's actually a parasitic organism that is out to mutate all life on the planet as part of its life cycle.
Literal green rocks appear in Super Karoshi, and as an obvious Expy of Kryptonite, they exist solely to take you out of your Super Mode. Since the object of every Karoshi game is to die, this is a good thing for you.
Prismere in Kingdoms of Amalur: Reckoning. This strange crystal starts out blue but turns an eerie blood red after absorbing magical power. The power provided by Prismere is enough to alter the Fate of living beings — something that is normally impossible. The main villains of the game the Tuatha Deohn use Prismere in everything — their armor, their weapons, and their shrines. This is bad, since fully charged Prismere also drives magical beings like the Fae completely insane. Mortals on the other hand can use Prismere equipment with no ill side effects.
The Facebook game Marvel Avengers Alliance is predicated on the falling to Earth of a substance known as Iso-8, which ... makes things better. There's a number of colours for different effects, it enhances all forms of energy manipulation, including physical, electrical, and mystical, Magneto's experimenting with it to make better mutants, etc etc. You can research it to make better Iso-8 (the ultimate variety enhancing all the character's attributes). That it's Phlebotinium is built into the game - there's no identifiable rhyme or reason to how it works so far, and probably the ultimate end game will have to do with what this stuff comes from. They've only opened 10 levels so far (with two more announced). Even the Special Operations missions, they still don't have a good clue on how Iso-8 works
The Marvel XP crossover game Avengers Initiative takes place around the same universe as MAA. The Iso-8 works in the same way, but there are less colors. You can upgrade your stats with the Iso-8, and it's implied in-game that Iso-8 is being used by Vault escapees and HYDRA to amp up their power and abilities. The only ways to gain Iso-8 are to defeat enemies and to mine them.
Minecraft has Redstone, a red dust that's commonly found deep underground. It can be used to make a compass, as well as a clock. Mix some into a potion and it lasts longer. Not to mention the fact that it can be used to make a wide variety of logic gates and digital circuits.
Nanites in Deus Ex. Super speed? Nanites. Being bulletproof? Nanites. Chinese lightsaber? Nanites!
In Realms of the Haunting green crystals appear in several instances, being shards of the Soulstone and usually serving the purpose of teleportation, as in you need one of these to meet the Gnarl, and later on to access Sheol.
Tedd's Transformation Ray Gun from the webcomic El Goonish Shive can temporarily (up to a month at a time) transform anyone into any other humanoid form (subject to failsafes). He uses a computer to program the forms.
Erfworld has the Arkentools, superpower magical artifacts created by the Titans that, when fully unlocked, grant their wielders tremendous power. There are four known Arkentools on the face of the Erf at this time, and only three have been revealed in the comic.
The Arkenhammer grants its user the ability to tame Dwagons as well as produce powerful lightning attacks. Its current wielder Stanley also found out that it also has the ability to turn walnuts into pigeons (and birds into walnuts) about twenty percent of the time. Stanley can also use the Arkenhammer to fly, though enemy forces suspect it's a poor kind of flight. Still better than none.
The Arkendish grants the wielder unmatched powers of thinkamancy (telepathy, mindcontrol, mind reading, etc.). It also grants its current wielder Charlie control of his Archons. Those who know Latin and watched TV in the '70s are now groaning.
The Arkenpliers' powers are mostly currently unknown, as they have only recently been attuned to their wielder. The single power they have demonstrated is perfectly raising a seemingly unlimited number of croaked (dead) units for no upkeep, no decay, and perfect obedience. In this world setting, that's a Game Breaker.
The fourth known tool has yet to be revealed. Fans temporarily refer to the unknown item as the "Arkensaw" when making predictions about what role they think it will play. A popular theory is that there are more Arkentools, nine total, one for each class of magic on the Erf axis. This is supported by Destructomancy, Thinkamancy and Healomancy being on that axis. Another theory puts the total at 27, one for each school of magic.
The Arkenshoes were revealed during one of the text-only prologue chapters. In addition to being the Ruby Slippers from Wizard of Oz (quite literally, as the characters involved were expys), they also grant their attuned user unlimited move. Considering that the citizens of Erfworld can't move out of certain areas unless it's their turn, and can only move so many hexes per turn, and that night time is never anyone's turn... in the hands of a powerful combat unit, they would be a Game Breaker. It's implied that they were used as such in the past. However, when their last attuned wielder used them to leave Erfworld, they left with her.
While the mutagen in Teenage Mutant Ninja Turtles (2012) initially seemed to have one specific use—to give whomever touched it the qualities of whatever organism they themselves last touched, as in the original cartoon—the ooze has since diversified, with it doing whatever the writers need it to do, such as turning squirrels into, essentially, xenomorphs from the Alien franchise.
Futurama: Bender's Big Score has "Torgo's Executive Powder" which is used for everything, from food to gunpowder substitute and plaster. This is made more bizarre by the fact that this power is made from ground up network executives. Granted, the cast of the show are fully willing to eat stupid sentient beings... Which explains their love of Glagnar's Human Rinds and Soylent Green.
Taking alongside Comics Lore, Nth Metal from Justice League. Immune to almost any form of magic, virtually indestructible and can be formed into insanely powerful hand-held weapons.
Transformers Prime has two. Normal energon, which is the life blood of all Transformers, is said to be the emanation of Primus that they use for almost everything. Then there's dark energon, which according to the ancient text is the blood of Unicron, which has the ability to revive the dead into zombies. In some continuities, Energon takes the form of of a mineral crystal that can be mined from the earth. Both of the above examples are like this (Energon is blue, Dark Energon is purple).
Hydrogen is useful, so is oxygen. What happens if we combine the two? We get plain old water. It is used to support every living being on this planet, its three states all have uses, steam to turn turbines, liquid water for everything, and ice for keeping lemonade cold for the hot summer days, it can clean off dirt and debris, make mud for the amusement of kids, cool the engine blocks of vehicles, make rainbows, and under enough pressure, can cut through steel. If thrown with enough force, it can also turn transparent the thin garments of busty ladies.
Petroleum. Not only is it a source of fuel, but it's also the feedstock for the chemical industry, including the pharmaceutical industry. Other major products made from petroleum feedstocks include all plastics, most rubber, and most commercial fertilizer. Plus it's the source of every major industrial lubricant, including synthetic lubricants.
Before petroleum, there was coal tar. Cooking coal produced gas for gas lighting before the advent of cheap electricity. And the resulting tar derived from the above process became the feedstock for early rubber products, early plastics, and artificial dye. Used up through the industrial revolution and WWI, until scientists and industrialists figured out that it was cheaper and more energy-efficient to use petroleum instead.
Carbon. It can form the shape of nearly any life form on earth. It's a major part of the aforementioned petroleum and coal tar. Coincidence?
Pushing this real-life trope a little further, Carbon Nanotubes are a subject in bleeding edge research. Carbon Nanotubes can theoretically be formed into efficient semi-conductors to build computers, can be formed to have tensile strength thousands of times greater than steel, can conduct heat more efficiently than copper, and is one of the best insulators from heat. Yes, it is both an insulator and a conductor, doing everything. They're expecting electrical, medical, mechanical applications, from batteries, to bike frames, to drug capsules. Perhaps this is a case of fact is stranger than fiction? And guess what Carbon Nanotubes are made out of? Pure Carbon.
The reason for both insulation and conduction is simple; nanotubes, like diamond, are amazing heat absorbers. If you had the money, diamond heat sinks would keep your computer running at something approaching room temperature — unfortunately diamonds are too brittle. nanotubes work on a similar principle, without the brittleness. And the presence of rudimentary nanotubes in Damascus steel (giving it its tremendous strength) is why the loss of the Damascus forging process is so lamented among both historians and metal workers.
Then there's graphene, another carbon derivative. It has excellent semiconductor capabilities, conduts heat, operates as a super-efficient filter that can trap even helium yet allows water through by having the water form molecule-thin streams that can fit through the graphene's structure... it's the next miracle material in industry. And the form of this amazing material? A super-thin honeycomb made of carbon atoms arranged in hexagons, forming a membrane so thin it's almost completely transparent. And yes, it has the same tensile strength at carbon nanotubes. Graphene research already progressed far enough to create graphene-based transistors (including the world's smallest transistor: one atom thick, ten atoms long) which are measurably superior to silicon-based ones, promising a breakthrough in the electronics industry. Also according to an experiment performed on a bottle of vodka as a joke, graphene can also make alcohol stronger by letting the water molecules through but not ethyl alcohol. The closest one can get to Applied Phlebotinum in real life, this thing is.
Metals. Notably copper, iron, and gold. Has been making everything from armor, weapons, cooking utensils, electronics, and currency.