This is really common, but I haven't seen a ubuntu howto for it, people more or less peice it together from posts and blog entries and the like.
So, here it goes. First off, make sure your system supports WakeOnLAN (WOL), if you know your system well, you already know if it does or doesn't.
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Automatic way:
This script does everything described in the Manual way, for you, except step 1 and step 4.
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The automatic method is super dialup friendly! thanks to gzip compression the filesize is a mere 1.5kb! almost half the extracted size of 3.4kb! 
1. If you havent already, go to your BIOS, and turn on WakeOnLAN (it varies, look for it.) If your network card is onboard, your set for step 2, otherwise there is probably a cable that should go from your network card to your motherboard, though this is not always the case.
Before continuing, note the interface you want to do this to. Most people know how to do this, if you do not, look at step 2a of the manual method.
2. Download and extract this: You can do it with the GUI and run the extracted program in a terminal by double clicking it, or open a terminal and do the following:
**** Removed dead link ****
3. As the exit of the program notes, now you just need to get/use a wake on lan sending program, like wakeonlan.
4. Sit on your lazy *** and have fun 
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Manual way:
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1. If you havent already, go to your BIOS, and turn on WakeOnLAN (it varies, look for it.) If your network card is onboard, your set for step 2, otherwise there is probably a cable that should go from your network card to your motherboard, though this is not always the case.
2. Back in ubuntu, kubuntu, xubuntu, w/e, we now need to make a script that will run every time the computer is started, because this command only lasts until the computer is turned on again once.
2a. Find out what network device you want to have the computer wake-able from, usually all, which is just one. If you have more network devices in your system, 9 chances out of 10, you already know what they are called.
You can NOT wake up a laptop or computer that is only connected via wireless with wake-on-lan, unless the bios has a method for this, this is very rare, and I do not garuntee this howto will work in such cases.
In your terminal, type:
You'll get something like: (I have removed my mac address for security)
Code:
eth0 Link encap:Ethernet HWaddr 01:23:45:67:89:ab
inet addr:192.168.1.2 Bcast:192.168.1.255 Mask:255.255.255.0
inet6 addr: fe80::215:f2ff:fe6f:3487/64 Scope:Link
UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1
RX packets:71495 errors:0 dropped:0 overruns:0 frame:0
TX packets:76190 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:1000
RX bytes:23164212 (22.0 MiB) TX bytes:7625016 (7.2 MiB)
Interrupt:217 Base address:0xd400
lo Link encap:Local Loopback
inet addr:127.0.0.1 Mask:255.0.0.0
inet6 addr: ::1/128 Scope:Host
UP LOOPBACK RUNNING MTU:16436 Metric:1
RX packets:1290 errors:0 dropped:0 overruns:0 frame:0
TX packets:1290 errors:0 dropped:0 overruns:0 carrier:0
collisions:0 txqueuelen:0
RX bytes:161182 (157.4 KiB) TX bytes:161182 (157.4 KiB)
So, I want this system to be wake-able from eth0.
2b. Now we create the script.
Note: you must be an administrator on the system you are doing this to.
Enter your password at the prompt.
Change to the startup script directory and start editing a new file:
Code:
cd /etc/init.d/
pico wakeonlanconfig
Paste, or type this into the file, replacing eth0 with your network device, repeat the ethtool line as many times for your devices before the exit line:
Code:
#!/bin/bash
ethtool -s eth0 wol g
exit
Set the permissions of the file:
Code:
chmod a+x wakeonlanconfig
Make the script run on startup:
Code:
update-rc.d -f wakeonlanconfig defaults
You should see something like:
Code:
Adding system startup for /etc/init.d/wakeonlanconfig ...
/etc/rc0.d/K20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc1.d/K20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc6.d/K20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc2.d/S20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc3.d/S20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc4.d/S20wakeonlanconfig -> ../init.d/wakeonlanconfig
/etc/rc5.d/S20wakeonlanconfig -> ../init.d/wakeonlanconfig
Now we finish by running it, and making sure there are no errors.
Code:
/etc/init.d/wakeonlanconfig
This should produce no output and put you right back at the prompt you started at.
3. Use it. you'll need something to send wake-on-lan packets with, "wakeonlan" is in the repos. And you'll need the mac address of the system.
To get your MAC address, on the same system you just enabled WOL on, type:
its the thing that looks like 01:23:45:67:89:ab , write it down.
turn off that system:
if your using wakeonlan from the repos, and you are on the same network as the computer your tying to wake up, replace 01:23:45:67:89:ab with your mac address and do, from another computer:
Code:
wakeonlan 01:23:45:67:89:ab
In MOST cases, you CAN SEND wake on lan packets from a wireless connected computer.
If that doesnt work, its likely the port on the system your trying to wake up isnt the default (9), try 7, or if your BIOS settings or book told you one, use that one.
Code:
wakeonlan -p 7 01:23:45:67:89:ab
If that STILL doesnt work, make sure wakeonlan is enabled in your bios and your hardware supports it.
*Note: It has been said that you need to disable -i from halt, however I have never had to do this, nor do I know how.
4. Sit on your lazy *** and have fun
Feel free to post any questions, suggestions, problems and I will tend to them ASAP.
Added notes:
* For this to work, most systems must be shut down properly, ie: with the power button or halt, or any of the ways to shut down. Unclean power-offs (like a power outage or holding the power button for 5s) seem to stop WOL from working untill the system is powered on and shut down properly. Though, there my be a few exceptions. This is a hardware issue with the BIOS. In my opinion, WOL should work regardless of how the system is powered off, but thats not the case. I suggest, if you have frequent power outages, that you have your BIOS set to Power ON after a power failure, most new systems allow this.
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