Despite the reference, the episode "Tick Tick Tick" isn't really a good example. The tick was visible to the naked eye, there was just one, and it didn't do anything but explode. But nano still sounds about a hundred times better. Just because it's big, doesn't necessarily imply it isn't made out of very small components, of course.
A better example of nanotechnology in the series could be the Hephaestus Project, a sort of living metal capable of repairing, modifying, and increasing in size when given the proper commands. Drakken used this technology in The Movie to create an army of robots disguised as toys.
The nanites have symbiotic relationship with the protagonist: if they go offline, he dies. Surprisingly not played for a plot point as often as one might think so much as an occasional inconvenience... until the show's entire third season, where the government forces the agency to disband after terrorists steal the generator and nearly wipe out the UN with it. It is implied that the main character is living on borrowed time without the full-size power generator, and that he will die in the near future with only the portable model to fall back on. Whenever he powers up, he's burning off said time. Nice Job Killing Yourself, Hero?
Big Bad Slade blackmails Robin into becoming his apprentice by infecting the rest of the Titans with nanomachines that will kill them if he should decide to activate them.
In "Crash", a computer virus somehow crates "drones" that are essentially this.
Alien nanomachines figure into the Justice League Unlimited episode "Dark Heart", and manage to give the entire League a serious run for its money. Later on, things really get serious when Brainithor gets a hold of that technology.
Brainiac/Luthor is also an example. Years prior to those events (back in Superman: The Animated Series), Brainiac forced Luthor to build him a new body, and his first act in that body was to inject Luthor with a "nanoscopic payload" that carried a dormant copy Brainiac's entire consciousness for safekeeping.
The DCAU version of Amazo the android was made of nanotech, which allowed him to evolve by duplicating whatever power he saw. Luthor and The Atom attempted to use this knowledge in an attempt to stop him, but he revealed that he had evolved beyond nanotechnology.
Deadshot is sprung from death row and recruited into Task Force X. To ensure he completes his mission and doesn't just run for the hills, he's been infected with explosive nanites that will literally blow his head off if he disobeys.
In the Code Lyoko episode "Amnesia", XANA creates nanomachines that act like a virus and erase the memories of anyone infected, spreading among humans as easily as a flu bug does. They are actually seen with a microscope, looking like minute spiders.
One episode of Captain Planet had a variation on the usual plot by having a mysterious figure appear in a small town in Latin America and give people everything they wanted, which it did by firing mysterious beams at nearby natural resources. Said beams turned out to be nanomachines. Unlike most examples, they were always under control of the villain, who turned out to be a spirit of environmental destruction whom the team had met before.
The second Teenage Mutant Ninja Turtles series featured a recurring antagonist in Nano, a nanomachine colony that had somehow "personified" (acquired sentience) and which possessed the emotional maturity of an infant. Eventually, however, it outgrows its immature tendencies and joins super-hero team The Justice Force.
Microbots create the first antagonist on Earth in Transformers Animated. A cockroach is injected with them, and it grows, bursts out of the tube it's held in, and proceeds to merge with everything metal around it and grow into a skyscraper-sized, tentacled, rather blobby monster. In a later episode, the Microbots are reconfigured to eat garbage, and again go out of control when exposed to an allspark fragment.
Central to the premise of Generator Rex. An industrial accident spread nanomachines all over the world and they have a tendency to warp living things into monsters, which the titular character must deal with.
In the Ben10live actionmovieAlien Swarm, the main villains of the film were a Hive Mind swarm of alien nanitie-like chips that were capable of infecting and controlling any living creature. They even had a queen. They weren't actually nanomachines, though, more like living microchips. Nano just sounds cooler.
Also, the brain uploading part was actually a result of an accident, as the Joker was using a device that was plugged into a machine to "convince" it to give him money. Batman destroyed the machine, leaving a copy of the Joker's mind on the computer and mentally stunning the real one for a few hours. Eventually, the digital Joker decided to upload his mind into Bruce's nanomachines.
The Powerpuff Girls had to deal with a swarm of carbon-devouring nanobots invading Townsville disguised as rain. The Professor shrunk them down to the nanobots' own size so they could actually fight. When the girls started winning, the nanobots merged into their equivalent of a Humongous Mecha...which the Professor just stepped on.
In Sherlock Holmes in the 22nd Century, a villain sends his victims puzzles that, upon being solved, prick them with a needle, injecting nanobots that cause them to temporarily go insane. Being a genius, Holmes doesn't take long to grasp the concept of nanotechnology, despite being born in the wrong century.
In one episode of Rick and Morty, Rick reveals that he put nanobots into Morty's bloodstream which when activated would allow him to, of all things, turn into a car.