The series Kiddy Grade bases a lot of technology on "Nano-mist" — a fog made up of trillions of nano-scale machines, which can achieve amazing effects — from keeping a 64 thousand kilometer long starship from collapsing under its own mass, to creating a barrier, to repairing damage, to terraforming a planet. Also known as utility fog.
It was suggested in-story (and confirmed in the sequel) that this is malarkey even inside the story; the ES members' abilities are not nanomachine-powered, but in fact seem to be actual (possibly Clarkian) magic.
The Fleet of Fog's ships (and their mental models) in Arpeggio of Blue Steel are assembled and repaired using nanomachines. The stuff's capable of mimicking organic matter down to the cellular level or creating neigh-indestructible battleships. Reverts to harmless silver sand when damaged/deactivated. Where it all comes from is one of the enduring mysteries of the series.
Mobile Fighter G Gundam's Devil Gundam has nanomachines known as DG Cells known for their three primary properties: repair, revival, and regeneration. DG Cells can infect living beings and turn them into willing servants; it can even resurrect the dead, as its Mecha Mooks are piloted by reanimated skeletons. Its creator intended for it to heal the damaged Earth, but after crash-landing its programming went nuts and decided to Kill All Humans.
Mobile Suit Gundam Wing mentions nanomachines in its world-building material, saying that creating the nigh-indestructable Gundanium alloy requires that level of fine precision. The sequel novel Frozen Teardrop uses them much more extensively, to the point where critics mockingly compared it to Metal Gear Solid.
The Turn A Gundam and Turn X's powerful Moonlight Butterfly attacks work by releasing technology-destroying nanomachines; since there's an implied link between the Turn X and the Devil Gundam (mentioned above), these nanomachines might be a development of the DG Cells.
Mobile Suit Gundam 00 uses nanomachines to explain why the crew of Ptolemaios can stay in space for extended periods of time and not suffer bone density loss and so on. They are also the explanation, together with genetic modification, on why Innovades like Tieria do not age.
GUNNM's Dr. Desty Nova is a specialist in Nanotechnology, and uses nanomachines to do almost everything — from healing almost any wound to making pudding out of trash. The manga even featured an extra section about the subject.
During the ZOT we learn that Mercury is a Grey Goo ball.
Taken to quite an extreme in Black Cat. One of the main characters, Eve, is a bioweapon of sorts who has several nanomachines inside her body that allows her to morph at will. This includes, but is not limited to, sprouting wings, turning her own skin into steel, transforming her hair into massive fists and, most notably, turning into a mermaid.
The plot of the Cowboy Bebop movie centers on these devices, which it frames as proteins that make its victims see thousands of butterflies before asphyxiating them nearly instantly.
In Trinity Blood, the Crusniks are super-powered über-vampires who feed on vampire blood. They transform from human form into Crusnik by activating the nanomachines in their blood.
Sky Girls has nanomachines as the focus of the entire story. Monster of the Week? Nanomachines originally built to cure medical problems gone rogue. Pilots wearing Latex Space Suit? They are protected by nanomachine armor that only lasts ten minutes note or twenty nine minutes, depending on which version you're watching. The weapons that the Sonic Divers carry? They are all nanomachine bullets.
Foo Fighters from JoJo's Bizarre Adventure — Stone Ocean is a unique character: while she does all the things a nanomachine-creature can do, such as healing herself and others and morphing her body to suit her needs (she has a literal handgun), she's actually a Stand-enhanced colony of plankton.
In Ghost in the Shell: Stand Alone Complex, nanomachines are widely used. In the first season, one of the potential treatments for cyberbrain sclerosis is based on nanomachines (although it isn't very effective). One episode also mentions that nanomachines are used to counteract air pollution. 2nd GIG introduces the "Japanese Miracle"; a nanomachine-based technology for neutralising radioactive fallout from nuclear explosions.
Though, being written before "nano" became a popular buzzword they're called micro -machines.
Viluy from Sailor Moon attacks with nanomachines. After one of Sailor Moon's attacks causes them to malfunction, they turn on their creator.
Yami from To Love-Ru apparently gets her powers from nanomachines.
As expected of an Eve-expy.
And now Yami has a 'younger sister', Mea Kurosaki with the same powers, presumably from the same source.
In Blassreiter, Amalgams/Demoniacs are created by nanomachines.
In GaoGaiGar FINAL, Palparepa uses nanomachines during his fight with Guy. After taking some damage from them, Guy uses his Evoluderabilities to rewrite the nanomachines and send them back at Palparepa. However, instead of weakening him the nanomachines have the unforeseen effect of making Palparepa cross the Bishonen Line.
In Deadman Wonderland, the Branch of Sin powers come from femtomachines called the Nameless Worm.
After suffering life-threatening brain damage that left her semi-paralyzed for months, Ai from Planetes finally get better after a long treatment involving nanomachines reconstructing neural pathways and such.
Science Ninja Team Gatchaman episode "The Particle Iron Beast Micro-Saturn" has tiny bugs coated in lead. They cover buildings, making it appear there's no radiation; later, they pull together to become a giant bug. Once it has hold of the Godphoenix, the bugs drop loose and start chowing down on the hull. They have to go to Hinotori to melt the things.
In Lupin III: Dead or Alive, nanomachines were left to guard Drifting Island (where the nation's treasury is kept) against thieves, and it has proven very effective, defeating Lupin's attempts to gain access twice before General Headhunter brought Olèander to blackmail Pannish. The nanomachines operate as a smart Booby Trap, chasing people and killing them.