Almost all of the species I keep have gone through artificial selection and as a result have different colorings from their wild counterparts. These different colorings are unique and make them easy to ID like my goldfish, koi, and bettas. However I also have brown kuhli loaches that all basically look the same. When it comes to things like that I just count numbers rather than individuals.
There are tracking tags you can implant in fish, but most are designed for fish larger than 6 inches. They range from radio trackers that allows you to pinpoint the exact location of a fish (these are typically used for large, ocean-going species) to small, bar-code like implants that can be scanned to reveal data on the individual fish when caught.
As far as the practicality of these tags to be used in the home aquaria, I don't really think there is any because they are expensive and inserting them properly takes a lot of practice.