What can I do to ensure that oracle database is shut down when the server reboots.
Do you mean if you type reboot at the command line? or are you meaning the init commands to reboot the system?
If it is with just typing reboot at the command line, there isn't.. This isn't the way a system should be rebooted. Using init is the best way.. Clean way to do it.
If you are using init 6. You can create a sym link to the oracle script that you use to start up the oracle database..
i.e.
ln -s /etc/init.d/oracle /etc/rc0.d/K09oracle
This will shut down the database before the system reboots or is switched off!
This is an example on Solaris.