The Command Zone is a zone used for special objects which affect the game like permanents do, but are not actually permanents. This includes emblems, plane cards, scheme cards, and the Commander in Elder Dragon Highlander. Commander 2013 and Conspiracy contain cards that interact with the Command Zone.
From the Comprehensive Rules
(Battle for Zendikar
(September 26, 2015
- 408.1. The command zone is a game area reserved for certain specialized objects that have an overarching effect on the game, yet are not permanents and cannot be destroyed.
- 408.2. Emblems may be created in the command zone. See rule 113, “Emblems.”
- 408.3. In the Planechase, Vanguard, Commander, Archenemy, and Conspiracy Draft casual variants, nontraditional Magic cards and/or specially designated cards start the game in the command zone. Each variant has its own rules regarding such cards. See section 9, “Casual Variants.”