Command
Commanders have access to an enviromental control menu which can be used to manipulate the time and weather. It can be accessed at any FOB through ACE Self Interact under Logistics.
Commanders have access to an intelligence menu which can be used to start secondary missions (as detailed here) as well as other intelligence actions to help out troops in the field. It can be accessed at any FOB through ACE Self Interact.
Commanders can name/rename FOBs which can be accessed by interacting with the FOB object, bringing up a small menu to name it.
Commanders have access to a guerilla support menu, providing the civilian reputation is above 0. This can be accessed anywhere through ACE Self Interact.