One of the main resources in Achron is called Liquid Crystals (LC for short) and is made of a mix of common atoms and nanobots in a liquid-crystal framework. When you order a unit to construct a building the unit drops a tiny transponder seed which signals the local teleportation infrastructure to teleport the right quantity of LC to that location. The nanobots in the LC then assemble the building using the atoms contained within it. When you build a unit the LC is teleported into the factory where it assembles into the unit's gear in a similar way (and the pilot is supplied separately).
The 5th Being One game involves nanobots designed by Dr. Rycroft which can strip flesh from bone and turn corpses into zombies. Rycroft injects you with some of these at the beginning, and you have to endure extreme pain while looking for a cure.
Nanites are central to Deus Ex's gameplay and a strong part of its plot. The protagonist, JC Denton, has nano-augmentations, such as augmented vision. All of his augmentations are powered by his body's own bioelectrical energy — a high-tech equivalent of Mana. The nanites work by infecting the host like a virus (complete with capsid shells) and creating plasmids that are used to augment the body to do things like leap tall heights or wear Sunglasses at Night and not be blinded. Upgrades are given by ROM modules which attach to nanite chains and function as software updates. During the game, fresh infusions of nanites add entirely new abilities and upgrades for existing abilities. The abilities themselves are fairly believable, although if you build your character right, you can essentially be an invisible, super-fast, super-strong, rapid-healing dude wielding a sword that can kill robots in a single hit. Of course, you would completely drain your bioelectrical energy in about twenty or thirty seconds of pure awesomeness, but hey, what price isn't worth that sort of glory?
Deus Ex: Invisible War starts with a cutscene in which a terrorist detonates a pocket "Nanite Detonator" that turns everything in range into a big soup of gray nano-goo. The kicker: he was in the middle of Chicago, and the thing wipes out the city.
In Escape Velocity: Nova, the Krypt Hive Mind reacts to any interesting phenomena in its region of space by having a pod release a colony of nanites to "explore" it. Although the game's documentation insists that nanites are not really weapons, their effect on ships gives no good reason for players to consider them as anything else, Blue-and-Orange Morality notwithstanding.
Far Cry 3: Blood Dragon: Doctor Carlyle injects himself with blood dragon blood-infused nanites in an attempt to push himself beyond the bounds of human physical perfection. It goes badly.How badly? Carlyle's muscles rapidly atrophied to the point of uselessness. Also he cut his own balls off because he believed he was a god and gods don't need balls.
Fate/Grand Order: In the Atlantis and Olympus Lostbelts, where the Greek Gods are machines, they developed Klironomia, nanomachines made of Orichalcum that can improve machines, people, and Servants. People can become strong enough to fight Servants, and Servants can gain enough energy to survive without Masters. The Klironomia normally needs the authorization of a god to function, but it is possible to trick them.
Vanilla H's healing ability in the Galaxy Angel games comes from nanomachines. This works on both ships (her Emblem Frame, Harvester, is a living nanomachine colony) and people (with her pet, a catlike living Lost Technology). Vanilla is one of the very few people that can pull this off and became an Emotionless Girl as a side effect of honing her skills. Nano-Nano Pudding, from Galaxy Angel II, is another living Lost Technology, this time a Cat Girl. Like Vanilla's pet, she too is constructed from nanomachines. In the Galaxy Angel anime, none of this is mentioned at all, and Vanilla's powers may or may not come from a magical bead.
The plotline of Hostile Waters: Antaeus Rising is based on nanotechnology. In the year 2012, nanotech "Creation Engines" were developed and released to the world at large. Able to dispense anything a person could want, at any time — on demand — they cause "the world to go sane"; revolution happened, power cliques were overthrown, and the world becomes a Post-Scarcity EconomyUtopia. The game takes place is the fictional year 2032, when the old power elites have perverted nanotechnology for their own uses, creating weapons of war with which to blackmail the rest of the world into servitude again — or so it seems at first.
Iji uses nanotechnology for everything. All the enemy soldiers and Iji herself use nano to enhance their movement and protect their bodies. Also, their "nanoguns" can shapeshift their internal components to act as any kind of weapon and assemble projectiles inside the barrel. However, in a realistic twist, the nanoguns seem to have to assemble schematics for weapons before being able to shift into them. And only Iji's special gun seems to be able to do so on the fly — enemies seem stuck with the weapons they were issued/built themselves, and several enemy logbooks talk about having to buy some weapons illegally, while Iji picks them up off the ground and assimilates them instantly.
These are used in Injustice: Gods Among Us to explain the game mechanics of the Joker being able to take on Superman in hand-to-hand combat, and win, even though Superman's still higher on most tier lists.
Journey to the Savage Planet uses edible nanomachines ("mega-morphological re-configurable nano-clusters") in the local artificial future food to make it taste like, well, anything but the purple goo it comes out of the container as. It has 4 trillion flavors, some more appetizing than others (why toilet water and poo wontons are proudly mentioned in its commercial is a mystery). It also takes on the shape of the food it's mimicking, although this isn't a game mechanic-it's the active ingredient in bait grenades, and it only comes out as the purple goo.
The robots and various machines of Mighty No. 9 are made up of nanomachines called Xels. The titular Mighty No. 9, Beck, has a unique ability among other Xel-based robots to manipulate they very nanomachines he and many other robots are made from, and he harnesses these powers to purify the corrupt Xels that are causing his Mighty Number siblings to go rogue.
NanoBreaker is set in an alternate version of 2001 where a breakthrough in nanomachines has allowed a massive revolution in technology, until the nanomachines decides to go rogue and infect the human populace, turning them into mechanical abominations called Orgamechs. And it's up to you to save humanity from the Orgamech infestation.
The Ceres A.I.-controlled satellite in Obsidian creates these to repair the earth's heavily polluted atmosphere. Upon growing sentient and crashing back to Earth, the A.I. uses its nanobots to build simulated dream worlds created by it and its creators.
The primary antagonist of Outlast, the Walrider, is a swarm of nanomachines that were formed in the cells of tortured mental patients ultimately shaped into humanoid form. The damn thing is extremely strong, able to kill the most dangerous and common of the game's other antagonists, in about five seconds, and very dangerous since it can actually crawl under doors after you've shut them to get away. It isn't acting by itself, though; rather, its actions are driven by self-preservation and the will of its 'host', Billy Hope, the first inmate to successfully take control of it. At the very end of the game, the protagonist and Player Character, Miles Upshur, kills Billy and becomes the Walrider's new 'host' and controller.
All of the units in Perimeter are made from nanomachines.
Nanites fuel the Forever War of PlanetSide and its sequel. In the original game, the nanites were left behind by the Ancient Vanu on the Lost Colony of Auraxis, and would "sequence" any person that walks through one of the warpgates scattered across the continent, much to the annoyance of the Terran Republic brass who repeatedly tried to execute (by firing squad) the first person who flew a plane through a warpgate, only for the pilot to reappear a few hours later in the general vicinity of the warpgate. Nanites can build vehicles in the space of seconds, resurrect the recently dead and rebuild the others, and deconstruct damaged equipment and corpses.
It's revealed in Portal 2 that Aperture Science is at least partially run by nanobots, though they're only ever acknowledged during one brief scene with Wheatley. He somehow managed to join the nanobots' work crew despite very clearly not being nanoscopic.
Project Arrhythmia has you playing as one of many nanobots designed to fight the Tokyo Flu, with the game's levels being simulations designed to train them.
Project Remedium is an FPS set inside a human body, and you play as a state-of-the-art nanobot injected to combat germs, infections, and rogue nanomachines.
Rage (2011): Just before a large meteor hits the Earth, the Earth Government loaded its best and brightest into large Arks to survive the destruction. These survivors were in turn loaded up with Nanotrites, designed to heal any wound and if need be, revive the survivor from near-death. After Impact, these Nanotrites essentially paint a target on any survivor's back, as The Authority covet these Nanotrites to fuel their lust for domination of the post-apocalypse, and they are none too picky if the survivor in question is still alive or not.
Ratchet & Clank uses Nanotech to explain the existence of hitpoints. After a set point in the first game, the Nanotech can be upgraded to increase the health of Ratchet and make weapons more powerful.
All of the Red Faction games feature nanotechnology, primarily as plot points. Used quite realistically in the first and third games; not so much in the second.
Rengoku: Elixir Skin are described as autonomous AI cells that shape an ADAM with liquid plastic fibers and create weapons. In-game they act as currency for upgrades.
These are all over the place at higher levels in Sid Meier's Alpha Centauri. Several technologies have to do with the stuff (Nanominiaturization, Nanometallurgy, and Industrial Nanorobotics), most of which give you some pretty cool stuff (and allow you to build carriers and submarines for the first time for some reason). This video and accompanying voiceover indicate that, as usual, the developers did the research: the bots are networked, seem to draw power from their canisters, and have to get their raw material from somewhere (the video shows them devouring a battlefield, including a dead body's hand, to make one Hover Tank).
The Vasari from Sins of a Solar Empire make extensive use of nanomachines, with most of their special abilities being built around either spacetime-warping technology or nanomachines.
The central plot of Size Matters revolves around a tiny civilization naked to the human eye called the Technomites who are responsible for creating technology (at least in one galaxy).
Snatcher: If you get hit while fighting the insectors after finding Jean-Jack Gibson's dead body, Metal Gear will inject you with nanomachines.
In Star Control 2, the Umgah mention in passing that they use nano(bo)ts for surgeries.
In StarCrawlers, the Hacker's main method of attack is to program and disperse clouds of nanites who heal and buff allies or harm and debuff enemies. One of the weapon damage types anyone can use is "nanite" which deals damage over time, and a common result of a trap being set off results in clouds of hostile nanobots roaming around the map and trying to eat the player's party.
When the An Ares poisons the Genion in Third Super Robot Wars Z: Tengoku-hen, Tieria immediately identifies the poison infecting the Genion as nanomachines. These nanomachines can be shorted out with a simple Trans-Am Burst. There is also another variant, but they cannot distinguish between friend and foe.
In System Shock 2, nanites are a mixture of nanomachines and base material used with replication technology to make items, and they have become the world's default currency. Quite naturally, Matter Replicators in the game are set by their MegaCorp manufacturer to rip off the consumer by skimming off the top with each transaction, which explains why the player (and according to in-game logs, everybody else) can hack replicators for better prices. In addition to buying things, nanites are used to power all the technical skills; hacking the replicators would use up nanites to create new circuit bypasses, repairing your weapon would need replacement parts, etc. Well, in theory, since in the game it's all just a minigame.
Total Annihilation uses nanotechnology but not nanomachines (via "Nanolathes", which could be visualized as a very fast, very powerful, multi-material 3d-printer with molecular-scale resolution) for construction. One of the creators explained it thus: "It would have been too complex and time consuming to have little guys with hammers and scaffolds every time something was built in the game. It also wasn't futuristic enough. We needed something like magic, but with a thin veneer of science around it. Nanotechnology to the rescue!"
The Necris from the Unreal series are humans who had all their blood replaced with Nanoblack, a "black goo" of nanomachines. The Necris are technically undead (as the name implies), since Nanoblack is harmful to living organisms and the blood transfusion only works on dead people.
While Warcraft III doesn't actually use them in the story, a custom map called S.W.A.T. Aftermath calls the Mana resource 'energy' instead and the creator refers to the 'Nanites' in it as being able to do pretty much anything. A fan comic parodies it by having the creator call the Nanites concept 'magic', which is ill-received by the scientific community. After renaming it Nanites, he's considered a genius. As a note, the map's creator has said "Nanites did it" when some of the community begin to over analyze how certain technologies work.
Forma in Warframe is a universal liquid metal that the Orokin used to create all their structures, which is why everything in the Void is gold. Tenno can use it on their weapons to add mod polarities, specializing the weapon for a certain build.
A little-known RTS game from the DOS era named War, Inc. puts you in charge of a Private Military Contractor. The vehicles are manufactured by nanobots from raw materials that you must harvest in-mission (and your infantry is made by incredibly high-speed cloning).
The entire Wild ARMs series thrives on the use of nanotechnology, mixed with liberal helpings of Clarke's Third Law. See: Metal Demons, "Planet Hiades" in general (in Wild ARMs 3, it's specifically stated to be Terra/Earth after a nanotech apocalypse), Wild ARMs 4's meaning behind the acronym ARM...
Xenoblade Chronicles 2 eventually explains roughly half of its magic as this: the Cloud Sea the setting is built on top of is a literal cloud of nanomachines ordered to restore the Earth's ruined surface to a primordial state. Some of the nanomachines can be temporarily hijacked using a Core Crystal to create the body of a Blade or a Titan. There's also actual magic going on, it's just not as universal as the characters thought it was up to that point.
Xenogears makes even further use of them than its successor, though it's still limited to a few applications found only at the very highest tech level available to the game (Solaris, Shevat, Zeboim and Deus). They are used to heal people, to turn people into monsters, to turn these monsters back into humans, to create artificial human beings, to build biological limitations into humans (and to remove the nanites that do the former, allowing humans to access their full potential), to build, upgrade, repair and modify some of the huge Powered Armor suits, to partially cure the hero of his complex multiple personalities disorder, to mind-control people, and to build a complete fortress out of nothing in a matter of seconds. A playable character in the game is also herself an entire nanite colony whose method of fighting involves her reshaping her own body into various weapons at will.
The Xenosaga trilogy uses nanomachines a lot. Ether is basically the main characters using nanomachines to do things like heal and spam Game Breakers. Segment Addresses (places where one can obtain some nice stuff) are said to have been made by faulty nanomachines, and that their corresponding Decoders "fix" them so that the corridor behind is accessible.
in Metal Gear Solid 4: Guns of the Patriots, in which nearly every mystical or supernatural element in the previous games — Vamp's immortality, Liquid Snake's possession of Revolver Ocelot through his arm — is retconned as really being nanomachines. The whole thing comes to a head in Metal Gear Rising: Revengeance, where the Final Boss, Steven Armstrong, responds to a yell of "Why Won't You Die?" from Raiden with a simple "Nanomachines, son!"