If you need a "nice" (ie orderly) shutdown, script it (shell, applescript, automator workflow, or any combination).

#!/bin/sh

. /etc/rc.common

StartService ()
{
# what to do on boot (can be empty)
}

StopService ()
{
# what to do on shutdown (can be empty)
}

RunService "$1"

This file has to be executable, i.e. chmod a+x filename. Then create a file by the name StartupParameters.plist with the following contents:

StartupParameters.plist
{
Description = "Name of your service goes here";
Provides = ("Whatever your service provides goes here");
Uses = ("Disks");
}