Command Target is an object that can respond to messages and issue commands, it achieves this by a series of Actions. An action consists of three parts: Message, Function, and Object. Message is a trigger condition like a mouse button press, release, etc. Function means do something. Object is Function's operand, according to different Functions, can be Sound, Shot, etc, or just null. See Actions Reference.
In the current version of Awakening, only Overlay & Shot is Command Target. When you select a overlay, the Properties panel will display as below:
Actions List is all actions of the Command
Add Action lets you add a new action to list.
Delete Action lets you delete selected action.
Transparent means this Command Target is disabled, doesn't accept any messages.