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Why are there two programs for that?

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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.

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X11 is not synonym of X. X11 is the current version of the protocol used in the X Window System and in existence since 1987. The other versions, from X1 to X10, existed during some period of the past, from the creation of X until the release of X11. – Juliano Nov 16 '10 at 12:53
Yes you are right, I fixed this. – echox Nov 16 '10 at 13:25
XFree86 was never the reference implementation, just the one that virtually all Linux & BSD distros shipped since it had far more drivers for x86 systems than the MIT/X Consortium/Open Group sample implementation. – alanc Nov 16 '10 at 20:59
What would you see as reference implementation before Xorg? – echox Nov 17 '10 at 10:03
Before X.Org the reference implemenation came from The Open Group, and before that the X Consortium. They provided X servers for a variety of Unix platforms and workstation vendors, including in some versions the XFree86 server for BSD & Linux distros. – alanc Nov 28 '10 at 0:09
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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.

XFree(3) is one of the functions defined by the X library, that is used to free memory allocations, just like free(3).

Perhaps you meant XFree86, which is a specific implementation of the X Windows System.

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