Latin for "an order within an order", the term in its most literal sense refers to any subgroup within another group, usually with its own set of leaders and command structures. A simple example can be found in most militaries: the generals control the divisions, while the sergeants control the platoons.
However, in most contexts, the term implies a subgroup that acts within the larger group structure, but is not beholden to the larger group's ideologies or practices - and usually works actively against them. Sometimes this can be benevolent (the many fifth columns of Europe, for example); many times it is not (the many coup d'etats of Latin America, for example.)
Most often the term is used to refer to secret societies with their own agendas acting in otherwise official capacities. Many Freemason conspiracies rely on the concept of imperium in imperio to explain themselves, and even today, groups such as the Illuminati, Bohemian Grove, and Bilderberg Group are constantly accused of using government, religious, and business institutions to promote their own itnerests and ideologies.