NetKernel can be configured to run as service. If you do this NetKernel will start and stop automatically when the server is booted and shutdown. This is usually the desired behaviour for a headerless server.
There is a script
netkerneld shipped inside the distribution jar
(both SE and EE) in the path
Steps to setup are:
update-rc.dand on RedHat search
When set up the usage is:
An updated version of NK3's windows service wrapper is available here...
Just expand this into your NetKernel INSTALL/bin/ directory and follow the steps in the readme.txt.
FYI because of the way the windows service wrapper works it will not be possible to use the "Reboot" NK option from the NK control panel when running as an NT service - you should use the Win32 services "restart" option to do a hard reboot.