An artist's impression of a hypothetical nanomachine interacting with a red blood cell.

From Wikipedia (shamelessly of couse):

Nanotechnology (sometimes shortened to "nanotech") is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with structures sized between 1 to 100 nanometre in at least one dimension, and involves developing materials or devices possessing at least one dimension within that size. Quantum mechanical effects are very important at this scale, which is in the quantum realm.
Nanotechnology is very diverse, ranging from extensions of conventional device physics to completely new approaches based upon molecular self-assembly, from developing new materials with dimensions on the nanoscale to investigating whether we can directly control matter on the atomic scale.

Generally in fiction, nanotechnology refers to nano-scale machines or robots which can manipulate molecules and atoms. After it became a popular staple of sci-fi, many authors tended to wank this concept to create nanotech which can do things that would be realistically impossible or almost impossible in real life. An example of this is the infamous "gray goo" scenario. Nanotechnology in fiction often serves as a magic buzzword or handwave to explain away ridiculous things, ignoring the feasibility of such a system in real life.

Still, in fiction, nanotechnology can be very broken, allowing for things like immortality, regeneration, and attacks that bypass conventional durability.

Fictions that make use of nanotechnology:

- Starcraft (Nanotech is used to help reverse Zerg infestation)
- Battle Angel Alita (Nanotech is very common, used for hacking and infecting/destroying biological and cybernetic organisms, even the entire planet Mercury was overrun by nanotech)
- Cannon God Exaxxion (Used for hacking, also to create androids/robots composed of nanotech colonies capable of shapeshifting and regeneration)
- Gundam (The Turn - A Gundam verse has the Moonlight Butterfly attack, which spreads nanites over interplanetary distances to destroy technology. It's also present in Gundam 00 for mostly sane purposes.)
- Mai-Otome (Nanomachines in their blood are what give the Otome their power)
- The Melancholy of Haruhi Suzumiya (Yuki Nagato has shown the ability to create nanotech to act as a proxy for her powers)
- Neon Genesis Evangelion (One of the Angels, although biological in nature, acted like a nanotech plague attacking NERV's computers)
- Saikano (Chise's powers are somewhat based on nanotech)
- Solty Rei (The plasma canopy that covers the planet is actually an artificial construct created and maintained by nanites)
- DC Comics (Nanotechnology is common in sci-fi oriented stories, The Atom has had to fight nanobots on several occasions)
- Marvel Comics (Again, common in sci-fi stories. Iron Man uses the stuff, as do many other earth and space - based characters)
- Wildstorm Comics (Several characters like The Authority's Engineer make extensive use of nanotech)
- The Culture (Most of the main races find conventional nanotech obsolete as they manipulate matter and energy directly with effectors)
- Doctor Who (Many examples, such as the Chula using nanogenes as medical devices capable of resurrecting the dead and rewriting the entire generic structure of a being)
- Futurama (Professor Farnsworth used some nanobots to purify some water but they eventually evolved into an entire robot civilization)
- Hyperion Cantos (Nanotechnology is commonly employed by the Technocore)
- Illium/Olympos: (Most of the upgrades given to characters such as Achilles and Diomedes are via use of nanotech)
- Stargate (Although the Replicators start out as macroscale blocks, they eventually evolve into nanotech creatures. The Asuran replicators were nanotech from the start).
- Star Trek (In one TNG episode a race of sentient nanites was accidentally created, also the Borg make extensive use of nanotechnology to repair themselves and assimilate other beings)
Star Wars (Appears sometimes, such as the mysterious compound known as "fizz")
- Terminator (The T-1000 and T-X, as well as several other technologies, utilize nanotech)
Warhammer 40,000 (The Necron technology and repair systems are mostly based on nanomachines. The life-eater virus dropped by the Imperium for Exterminatus is also presumed to be some application of nanotechnology.)
- Xeelee Sequence (Humans and likely other races used it, at one point a runaway nanotech disaster consumed one of the solar system's outer moons)