Since FreeNAS 9.1.0
--------------------
# mkdir -m 0755 /data/bin
# cp hdd_spindown.sh /data/bin/
# chmod 0755 /data/bin/hdd_spindown.sh

In GUI add init script:
  Type    = 'command'
  Command = '/data/bin/hdd_spindown.sh -d'
  Type    = 'Post Init'

Prior to FreeNAS 9.1.0
-----------------------

ISSUE THE FOLLOWING COMMANDS ONLY IF YOU KNOW WHAT YOU'RE DOING!

# mount -uw /

# cp hdd_spindown.sh /data/
# chown root:wheel /data/hdd_spindown.sh
# chmod 0700 /data/hdd_spindown.sh

# cp hdd_spindown /conf/base/etc/rc.d/
# chown root:wheel /conf/base/etc/rc.d/hdd_spindown
# chmod 0755 /conf/base/etc/rc.d/hdd_spindown

# cat << EOT >> /conf/base/etc/rc.conf
hdd_spindown_enable="YES"
EOT

# mount -ur /
