Refers to a system for evaluating or discussing another system. Metazoology, for example, would presumably be the examination of zoological methods as (hopefully) a valid system.
In the original Latin it meant 'after', and thus Metaphysics means 'after', or 'beyond' physics, not 'about' physics.
It is now often used as a cute way of referring to something that is in some way self-referantial or self-containing. A metacorporation is a corporation formed from corporations. Metadata is data about data. Metacognition is thinking about the fact that you are thinking.