Both are metapackages but xubuntu-desktop is a metapackage for much more stuff than the other one that is just for the desktop environment, xorg and few minor things.
You can read about the difference between a package and a metapackage here.
In short metapackage does not contain anything else than references and what matters is what metapackage refers to (metapackage claims to depend on them and asks that list to be installed).
So I guess your first option would not install anything. If you really want the minimal solution then go with xfce for which the correct command would be:
sudo apt-get install xfce4
Just add anything else one by one according to your needs. Also if you have xfce4 installed you can always expand your install with xubuntu-desktop that would just add lots of stuff.
You could also consider using Webmin or Zentyal for web based server management.
They are not different
Suppose you have already installed Ubuntu and want to try Kubuntu. Most of the stuff is already there. Install the Desktop Environment (DE), option 1.
Now you have both. Each DE comes with some default applications. You can use any application in any DE. You can log out of one DE and log back into the other DE. Your files will be in the same place, just the environment will look and work different.
Now suppose you like KDE better and don't like Unity. You have another computer, and you want the KDE on that one. Install Kubuntu directly on the computer. Go for option 2. Kubuntu uses the KDE Desktop Environment, Ubuntu uses Unity by default. But they are both the same distro (Ubuntu).
Default Applications
The default applications are different in different DEs. Some DEs have more common default applications than others. For example Unity and Gnome have many common default applications. The default applications in Unity and KDE are somewhat different. If you start with Unity, and install the Kubuntu-desktop, option 1, you will have the default applications of both the DE.
If you go for option 2 and install Kubuntu, you can still install some default applications of Unity if you like them better. For example, you can install Firefox, the default browser in Ubuntu in a fresh Kubuntu installation.
The difference between the flavors are in the set of packages installed. However, all flavors of Ubuntu use the same repository for downloading updates, so the same set of packages is available regardless of which flavor you have installed. New flavors have to go through a process to become a Recognized Flavor.
Reference: Ubuntu Flavors
Hope this helps
Best Answer
There is an xubuntu live (desktop) cd available here :
http://xubuntu.org/getxubuntu/
xfce is a desktop environment , see http://www.xfce.org/ and http://xwinman.org/
So when you install xfce you get xfce.
xubuntu, however, is an additional set of packages and customizations to make the xfce experience more rich. xubuntu-desktop is a meta package and you can see the entire list of packages here
http://www.ubuntu.com/about/about-ubuntu/derivatives
As you can see the list includes xfce + a number of additional packages.
See also https://help.ubuntu.com/community/Installation/LowMemorySystems#XFCE
Use which ever you prefer, from your post I would suggest you stay with Ubuntu (unity).