Meta- originally meant beyond, or after. This is the sense it's used in metaphysics. Were this word coined today, it would probably be 'postphysics', rather than metaphysics. Meta- is often still used in the sciences in this original sense.
In medicine meta- often means behind; the metatarsals are behind the tarsals
Nowadays it has a new meaning: a second level of order, self-referential, x of x. See: Metacognition (thinking about thinking); Metanodes (nodes about nodes); Metadata; data about data.
Meta- comes from the Greek preposition meta (μετα) meaning "in the midst of", "among" or "with", which also came to have the meaning "after".