I remember that at one place we used to have users edit their autoexec.bat and disable all sorts of programs like network connect and anti virus (this was around the time of the "I love you" virus.
We had to hide the Autoexec.bat so what we did was changed it's name from Autoexec.bat to reboot.com but it would work because someone discovered that you could have your autoexec start as follows
then the bat script
then some wierd characters at the end which was the reboot.com code (4 bytes only )
then we used the assembler to edit command.com and change the string AUTOEXEC.BAT to REBOOT.COM and it was all ready to go.
Reboot.com rebooted the machine
and the boot script remained hidden.