What countries have a theocratic government?

A theocratic government is one where the Religion and the State are the same - that is, all government functions (and decision-making) is done by the religious hierarchy. This is distinct from the concept of a State Religion.

Currently, there are really only one real theocracy in the World: Vatican City.

Iran has a strange mix of theocratic and democratic elements. Likewise, Saudi Arabia has a mix of theocracy and an absolute monarchy.

Israel has a State Religion with some influence over the secular government, but even that portion really isn't a theocracy (as the State Religion isn't organized in such a manner as to be able to exert institutional influence).