Shortly before the events of the main series, the world of Gundam 00 was subject to the "solar power wars". When advanced solar technologies were discovered, oil suddenly became relatively worthlessnote In real life, fuel is in no way the only important use of oil. For example, it is also essential to the manufacture of plastic. Fuel is simply what consumes the largest amount of oil., leading to a number of Middle Eastern countries continually splitting apart into new ones. To harness the technology, countries needed to build space elevators, and this lead to blocs of nations forming who jealously guarded their elevators and were constantly at the brink of war with the other blocs.
All Phlebotinum in District 9 has a biological component, so while everybody is stockpiling BFGs, only the slum residents can use them.
Played for Laughs in Water (1985), about a Caribbean island that strikes mineral water, causing the intervention of various outside governments trying to seize control of it.
Dune had its Spice, a resource so vital that whoever owns Arrakis, the only planet that produces it, will have huge power over other planets. Several novels have story arcs where someone attempts (unsuccessfully) to break the Arrakis monopoly on spice by transplanting a Sand Worm to another planet, creating a spice substitute, etc.
There is eventually a successful attempt not at breaking the monopoly, but at devaluing Spice. One of the reasons it is so important is that it is essential for FTL navigation. Eventually one faction manages to develop an alternative navigation method.
Pynvium in Janice Hardy's The Shifter can absorb pain. Its mines are important enough to fight over, but it is when the healers run out of it that the plot kicks in.
The war driving the plot of The Flight Engineer started when the Mollies cut off all exports of anti-hydrogennote they had discovered a vast field of naturally occurring anti-hydrogen, rendering particle accelerators obsolete to the Commonwealth. Their intent was to cause the Commonwealth to collapse (due to religious objections to their way of life) since the Welters can't trade between planets without A-H. The Commonwealth was forced to make war on the Mollies for their very survival.
The Tomorrow War trilogy by Alexander Zorich after a few preludes and interludes, is centered on the war between United Nations (Earth and affiliated planets) and Concordia (ones returned to Zoroastrianism and churning out clones for colonization and military purpose) fought mostly over a planet owned by the latter power, which was rich with naturally occuring jump fuel mined much cheaper than synthesis of the same.
The conflict and political situation in the Star Wars Expanded Universe novel The Bacta War revolves around the eponymous miracle medicine, which is produced only by the planet Thyferra, recently seized by the Big Bad. Worse, the villain previously arranged to unleash a plague on the city-planet Coruscant, which can only be cured by bacta — which she is all too happy to sell them, at prices that threaten to bankrupt the fledgling New Republic. Her plan is to either drain the Republic's coffers, or force them to cut back bacta distribution, driving a wedge between humans (who are immune to the disease) and aliens (who are vulnerable). She counts on them not responding militarily because she's not a dictator for them to overthrow but the elected leader of Thyferra; conquering a (nominally) democratic world would run the risk of other planets breaking away from the New Republic. It doesn't work, chiefly because Wedge and the Rogues are able to undertake a massively successful guerrilla campaign against her, bankrolled largely by stolen bacta. (For added irony, the start-up funds for their campaign came from bank accounts the villain set up in one the heroes' names in a failed effort to frame him as a traitor.)
The Way of Kings, first book in The Stormlight Archive, has traces of this. For the past six years, the war between the human kingdom of Alethkar and the Humanoid Aliens known as Parshendi has been a stalemate, for after the Parshendi assassinated King Gavilar of Alethkar—on the very night they signed a treaty of alliance with him—they fled to the Shattered Plains. While the human armies would be at too great a disadvantage if they attempted to attack the Parshendi redoubt at the center of the Plains, both the Parshendi and the humans need the gemhearts grown within the chasmfiends that live at the Plains' outer edges to fuel the Magitek that feeds their armies. Thus, the humans have been fighting the Parshendi in a war of attrition over the gemhearts for the past six years, and are steadily winning.
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In the Star Trek universe, the Klingons and Federation sometimes fought over sources of dilithium crystals (e.g. the Star Trek: The Original Series episode "Elaan of Troyius"). In Star Trek IV, Scotty and Spock invent a way to "recycle" it with particles stolen from "nuclear wessels", thus making it less rare by the Next Generation era.
In an episode of Star Trek: Voyager, a planet was raided for deuterium. The writers didn't do their research... although given the existence of things like the Oklo natural nuclear reactors in Gabon, who's to say that there isn't some way the planet could have produced and/or received abnormally large amounts of heavy hydrogen? Though the technology to convert protium (the most common hydrogen isotope and thus the most common substance in the universe) into deuterium is well-established in the Star Trek verse, so the ship running critically low on deuterium in the first place would require epic-level incompetence.
In the first Star Trek Shatnerverse novel, Chekov and Uhura are engaged in an undercover operation and pretend to deal with a shady Klingon. He offers dilithium as payment. Chekov brushes him off, saying it is nearly worthless now, ever since the whole "nuclear wessels" discovery (i.e. ships can run forever on a single set of dilithium crystals without needing to replace them).
Somewhat bizarrely, in Star Trek: Voyager, the Kazon, an oxygen-breathing species traveling in hydrogen-powered ships, will kill, steal, or trade hostages for water. When he first arrives on the ship, Neelix seems similarly surprised by Alpha quadrant water technology.
That's mainly because the Kazon are Too Dumb to Live. The Borg refuse to assimilate them because of that. They're the only known species that the Borg have deemed to have absolutely nothing worthwhile to add to the collective.
A classic Doctor Who had one of these, in the episode "The Caves of Androzani". It was over spectrox, "the most valuable substance in the universe."
Mentioned in the partially war-themed Pink Floyd song "Us & Them":
And who'll deny it's what the fighting's all about
The flammable substance promethium is critical to the war machines of at least three factions in Warhammer 40,000: the Orks, the Imperium, and Chaos. Expect frequent conflicts over promethium mines and refineries, since the Imperium is the only group that bothers to build them instead of just stealing the stuff from everyone else. One such conflict can be found in the novel Caves of Ice, which has the 597th Valhallan deployed to fend off an Ork attack.
Space 1889 liftwood is by far the most important resource on Mars, giving air supremacy to the party that can deny it to his opponent. It is by far the most important reason humans are on Mars and also a driving force behind the intra-Martian conflicts. This is somewhat subverted in that no state can really directly control this resource since it grows on high mountains controlled by the bestial High Martians. The main book also states that the Bhutan spice is controlled by Boreo-Syrtian league that trades exclusively with the British. Maintaining this monopoly is an important aim for the British, apparently even making the normally very anti-slavery British of late 19th century overlook the fact that it is exclusively grown by slaves.
The whole BIONICLE story has its roots in the Core War, a massive world war over Energized Protodermis that emerged from the core of the planet, the unstable nature of which ended up splitting Spherus Magna into three.
The Command & ConquerTiberium series revolves around an alien crystal that's extremely rich in resources, leading to several Tiberium Wars fueled by or fought over the stuff. Of course, it is the fight against tiberium that's the real danger...
Humans fought a really big war over Imulsion in the Back Story to Gears of War, before the scary underground alien invasion.
"Ragnite" was one of the reasons behind the war in Valkyria Chronicles, with the player's small neutral country caught right in the middle due to its large natural deposits of it.
Practically inevitable in the later installments of Civilization if you want your faction to prosper, unless you get really lucky with city placement or allies. If you do not have era-appropriate strategic resources, expect to be invaded by other civilizations who do and consider you easy pickings. If you have era-appropriate strategic resources, expect to be invaded by other civilizations who do not have it and desperately want it. Either way, wars are almost certainly going to be fought over it.
Final Fantasy VII features the miracle substance Mako. Generated from the essences of creatures long-since dead and pumped from the ground, it has allowed the company controlling it to control world politics, and its overuse creates serious consequences for the planet... similar to a certain black substance that the people of Earth have been using for several decades with similar results. This certain black substance is later treated as a viable alternative to mako in Advent Children.
There's a bit in Shinra's headquarters where they have a set of advertisements for the line of cars that they make (represented during the opening FMV). The video clearly shows the engines of said cars using Mako in a way that is analogous to the use of the... distillates of the aforementioned black substance. (And "The Aforementioned Black Substance" would make a great band name.)
The Fallout series' backstory mentions conflicts over the world's dwindling oil reserves between the 2050's and 70's. The European Coalition invaded the Middle East once oil prices rose too high, though these Resource Wars ended suddenly once the last of the petroleum in the region was tapped out. With Alaska containing the last oil on the whole planet, China invaded America in a conflict that led to a global nuclear war, hence the game's post-apocalyptic setting.
The main conflict in Fallout: New Vegas is over Hoover Dam, a significant source of electric power in the region. In addition, Father Elijah is willing to spend any amount of blood (except his own) to get his hands on the phlebotinums found in Dead Money. He likewise sacrificed nearly all of his Brotherhood soldiers trying to hold Helios One (a solar power plant) against the NCR until the remainder decided the current plan was suicide and retreated against his orders.