Command is a short hand for the built in Command Line tools (or CLI) in Magento 2, the custom CLI tools made for Magento 1 or other actions that are executed on a Magento site using the Command Line (i.e. the Terminal application for mac) when logged into a server with SSH.
In every version of the Magento application the user has the ability to execute commands for the application using different command line tools. In Magento 1 the most popular tool is the n98 magerun cli tools that gives the user the ability to control all aspects of the application from the command line. This included turning on template hints, re-indexing the site, creating admin users or even using the tool to execute test lines of PHP.
In Magento 2 the system can with a built in CLI tool that performs many of the same functions as magerun but has a deeper integration to the platform and allows the end developer to create their own CLI commands to work with Magento (this system is based on the symphony command line tool).
But outside the Magento application CLI tools, this tag can also relate to execution of bash or shell scripts. In Magento 1 you are able to able to execute shell scripts that ship with the code to reindex the site or enable, clear and disable the compiler.