The Control Center is used by GNOME to customize the user's desktop environment according to his preferences. It consists of a bunch of configuration dialogs through which the user can set his preferences for particular parts of the GNOME environment. As an example, the desktop's background color, mime-type handling and mouse properties are all handled there. The Control Center comes with an easily extendible system which allows you to add you own configuration dialogs.
Generally, only things that are modified by the user for his environment are appropriate for inclusion in the Control Center. A joystick configuration dialog would be a good candidate, while configuring the system's NFS export table is not. In addition, applications should restrict their configuration options to a GNOME property box, instead of allowing external configuration. Finally, if you are setting something up for the first time, a Druid might be better used.