We have a CentOS 6 VM running apache with several virtual hosts. One (and only one) of these was intermittently not working.
What I was seeing was that after an apache restart sometimes you get an index listing, other times you got our intranet site. Even weirder - The example virtual host that gives you a directory list was disabled! Even more strange was that the server aliases I have set up for the intranet site, always worked.
On CentOS 6 at least - apache is gracefully restarted automatically every so often.
The temporary fix to get our intranet site back - was to restart apache.