Nanites are machines incorporating nanotechnology. This means, roughly, that they are very small. A nanite can also be called a nanomachine.
Because the effect of one nanite on anything substantial is, well, likely to not be very substantial, they're usually conceived of as working in large groups.
In theory nanites are very useful; you can use them to do all kinds of fiddly work at a very fast pace with much greater subtlety than human tools. However very few nanomachines are actually in use in comparison to the range that is represented in science fiction.
The scariest type of nanites are those that have a tendency to acquire intelligence and/or overwhelm and disassemble unconsidered trifles like people or the earth in their quest for resources to reproduce themselves. You have no idea what the little buggers could be up to because you can't see them until it's too late!