Reboot
sudo reboot
Shutdown
sudo shutdown -h now
sudo init 0 (this has the added advantage of turning off the TXD GPIO pin)
Reset Switch
On the newer Raspberry P'i's there's unused points on the motherboard labeled "P6" that can be used as a hard reset switch. See http://raspi.tv/tag/solder-a-p6-header-on-raspberry-pi