I have a Linux based (Debian 5.0) NAS that I need to shutdown reliably. When ssh'd into the NAS box I issue the following command:
sudo shutdown -h now
I've also tried 'poweroff' and su'ing into root and running the commands with the same results. It shuts down all the processes and everything fine but does not always 'halt' the system. I need it to power down into the S3 state so that I can reliably use Wake On LAN to start the unit as needed. For what it's worth, wol works great and works every time as long as the unit is in it's S3 state.