Is Ubuntu Server an operating system or an add-on for Ubuntu? Also any info on setting up a minecraft craftbukkit server would be nice.
You can download Ubuntu Server from Ubuntu's website and you can also install it as add-on in a ubuntu installation.
I suppose that you want a GUI support for your server, so you should go with the add-on part.
If you want an apache server you will have to install apache.
As for craftbukkit server - link - does not require apache AFAIK.
About minecraft servers on Ubuntu: My friend told me that minecraft no longer supports ubuntu, but it will work if the server is cracked. Good luck. (editor: i doubt it. a config makes it possible to play "online mode" or "offline mode" nothing to do with ubuntu)
Ubuntu Desktop = linux kernel+GUI (unity) + apps + stuff
For a home minecraft server, which starts and stops at boot and shutdown, you could try this script: http://www.minecraftforum.net/topic/121830-multi-world-linux-minecraft-server-control-script/
For a normal minecraft server, you should use Aleksandar's link:
(I recommend using "screen" either way, with that, you can put anything in the background while you can do other stuff, extremely handy for ssh connections)