Using gksu vs. sudo
Commands (in the command line terminal) that require administrator or root privileges must be preceded by sudo, or the graphical version, gksu. For most uses, the commands are interchangeable and either can be used.
However, there are some subtle differences. Specifically, gksu launches with the root configuration files, while sudo launches with the user’s configuration files.
http://www.psychocats.net/ubuntu/graphicalsudo
Here is a nice discussion. This discussion recommends gksu for all uses except when a purely command line environment is being used, such as when there is no desktop environment installed. In that case use sudo.
In this guide, both are used. When commands are applicable to both the server-only versions of Ubuntu as well as the desktop versions, sudo is used. However, in a Gnome desktop environment, gksu can usually be substituted.
(Note: gksu is the version of sudo for use in Gnome, the default desktop for Ubuntu. For Kubuntu (KDE) users, use kdesu instead.)
