There are a number of different ways to restart your Apple TV. Depending on your setup, each one has it's own benefits. I've listed a few of the different methods below.
MENU + DOWN
If you press and hold the MENU and DOWN button on the Apple TV remote for 6 seconds, the Apple TV will perform a complete reboot. Some people have mentioned that a downside to this is if you are running a tethered jailbreak you will have boot the device back up tethered. If you are running an untethered jailbreak - like GreenPois0n RC6 or newer - then this is probably the simplest method to reboot your device as it only requires the remote control.
SSH: killall AppleTV
This method requires you to SSH into your Apple TV using a client like Putty (or a Terminal) and issue the "killall AppleTV" command. Please note that the command is case sensitive. The benefit to this method is if you are running a tethered jailbreak, you will not have to get out your computer to do a tethered jailbreak. A downside of this method is it only works if you have a network connection to your device and you have to have a PC or other device to issue the command.
Pull the Power Plug
This is probably the most drastic method of all the ones I'll list, but it works in a pinch. As you may expect, some people claim that using this method may be bad for your device. I personally try not to pull the plug on any of my devices, but I've occasionally had to use this method. If you are running a tethered jailbreak, this method will also require you to get out a computer to boot tethered.