I have a Centos 4.2 server with Apache 2. My original problem was that
Aliases did not work. You can browse to a domain, and enter a configured
alias like, domainname/aliasname, and it will display the index page of
the domain without errors, but never complain about the alias. Actually,
you can enter anything after the domain name and not get a 404 response.

Now, I am finding that if I add a new virtual domain .conf file
in /etc/httpd/conf.d it over-rides what is already there, so when
browsing to  a.domain.com and b.domain.com, you get b.domain.com. If I
remove the new b.domain.com conf file, a.domain.com works like it
should.

I am sure it a simple omission or addition in httpd.conf, but I haven't
figured it out.