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It depends on what version of XFree86 you are currently running, if it is 4.x.x then it uses XF86Config-4 file, otherwise XF86Config, the reason both files are there is that some video hardware has better support in XFree86-3.x.x version which uses in RH systems (and many others RPM drivern distros) XF86Config file; another reason it is left out for history purposes like it happens with apache originaly there were three configuration files and now it is only one but you still see three files included with apache these were access.conf, httpd.conf and srm.conf now they are all part of bigger httpd.conf.
right X3 ALWAYS uses XF86Config, X4 Will use XF86Config-4 *IF* it exists (i.e. you are also using X3 potentially) OR XF86Config if the other does not exist. if you have not got X3 installed then delete -4 and use the normal one fine.
It's not the name of the file that determines which version of X it is for, its the syntax. XFree86-3.x.x uses a difernt syntax to XFree86-4.x.x. Distro's that offer the option to install v3.x.x and v4.x.x include two copies of XF86Config, one with the correct syntax for v3.x.x called XF86Config and one for v4.x.x called XF86Config-4.