Type "fmsadmin" at the command line and it will walk you through the help system.
You can use these following commands:
To close the databases:
To list the status of the databases:
fmsadmin list files -s
To stop FileMaker Server:
fmsadmin stop server
Hopefully, this helps.
Is there a Windows equivalent of this? The one in /fmserver/common/java/bin/ doesn't seem to do anything when run from the cmd.