Vanilla H's healing ability in the Galaxy Angel games comes from nanomachines. This works on both ships (her Angel Wing, 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 the later games, is another living Lost Technology, this time a Cat Girl. Like Vanilla's pet, she too is constructed from nanomachines.
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 the Galaxy Angel anime, none of this is mentioned at all, and Vanilla's powers may or may not come from a magical bead.
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.
Total Annihilation uses nanotechnology but not nanomachines (via "Nanolathes", which could be visualised 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 plotline of the video game Hostile Waters: Antaeus Rising, by Warren Ellis, 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 Utopia. The game takes place is the fictional year 2032, where 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...
Deus Ex - Nanites are central to gameplay and a strong part of the plot. The protagonist, JC Denton, has nano-augmentations, such augmented vision. During the game, fresh infusions of nanites add entirely new abilities and upgrades for existing abilities. All his augmentations were powered by his body's own bioelectrical energy — a high tech equivalent of mana. The abilities themselves were fairly believable, though if you built your character right you were essentially an invisible, super-fast, super-strong, rapid-healing dude wielding a sword that could 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 glory?
The sequel, Deus Ex: Invisible War, starts with a cutscene where 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.
Sid Meierís Alpha Centauri. All over the place at higher levels. 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 hovertank).
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.
Also the game Size Matters central plot revolves around a tiny civilization naked to the human eye called the Technomites who are responsible for creating technology (at least in one galaxy).
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.
The spiritual predecessor, Xenogears, makes even further use of them, 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.
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, replicators in the game are set by their Mega Corp. 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.
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.
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.
Though 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.
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, the fourth game's meaning behind the acronym ARM...
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.
In Cyberstorm, a Turn-Based Strategy game set in the Earth Siege universe, you can buy your HERCs self repair systems based on nanotechnology.
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.
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.
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.
A little-known RTS game from the DOS era called 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).
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 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 units gear in a similar way (and the pilot is supplied separately).
Nanites fuel the Forever War of PlanetSide 1 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 appear a few hours later in the general vicinity of warpgate. Nanites can build vehicles in the space of seconds, resurrect the recently dead and rebuild the others, and deconstruct damaged equipment and corpses.
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 it's 'host', Billy Hope, the first inmate to successfully take control of it. At the very end of the game, the protagonist and PC, Miles Upshur, kills Billy and becomes the Walrider's new 'host' and controller.