Track small differences in 5 files with Mercurial?
I don't think you can; that's not a common thing to do in a VCS.  If I'm wrong, I'm happy to be corrected.
Perhaps you can make the "master" httpd.conf file a template, and have a build script that generates the five files you want, passing in the appropriate port number for each file.  That way you isolate the change points in your file, and keep the common bits, well, common.  There are reams of templateing languages out there.  Or you can simply use sed.  Or do as nmichaels suggested and use Apache's capabilities directly.
There are lots of ways to skin this particular cat, but I don't think Mercurial is going to help you directly.
I have five httpd.conf files which differ only in the port number that they are listening on. All of the other data between the sites is the same. Is there any way to track this as a single file in Mercurial? So that if I make a different change to the httpd.conf file, I could push this to all five, and keep the port numbers separate.
Thanks,
Kevin