Why are there two programs for that?
X refers usually to the X Window System, a networking protocol and a software which supports drawing application windows on your screen. Another synonym for the protocol is X11.
XFree86 was the reference implementation of the X Window System until 2003 there was some trouble concerning the license for the new release, which was seen incompatible to the GPL from many developers.
They left the XFree86 project, founded the X.Org Foundation and created X.Org, which is another implementation of the X Window System.
The development of XFree86 still continues.
X is short for X Window System, which is the architecture specification and protocol that allows Unix graphical applications (clients) to connect to a display (server) in order to display the GUI and interact with the user.
Perhaps you meant XFree86, which is a specific implementation of the X Windows System.