Empyrion is a game currently in Alpha. So, this list may be updated over time, as the game progresses. Currently, there is only a few commands within Empyrion. You've got your standard godmode and ban commands, but there are a few others worth taking a look at.
The Console is opened by pressing the ~ key, and gives access to various commands from switching world gamemode type, to debug commands, to other creative options. Commands may require elevated permissions in order to use them, these commands are marked as being a GameMaster, Admin...