UPDATE: I found a work-around that has allowed me to get back 2 of my 3 virtual hosts.
Background: The "NameVirtualHost" fix alone was not working for me. I upgraded from Snow Leopard Server and no place I put NameVirtualHost would enable my <VirtualHost my.hostname.com:80> to work.
I read an apache.org website about VirtualHosts and DNS errors that says that a VirtualHost definition may be ignored if Apache cannot resolve the VirtualHost/ServerName to an IP address. My testing seems to indicate that my VirtualHost directives are just being skipped, so I tried putting in my static IP for the <VirtualHost> and then using the ServerName to specify the hostname for the virtual host. In addition, I added the 00000_MoreTestingRequired.conf file and added a NameVirtualHost line for each hostname.
Now several of my subdomains are working again! The only remaining issue is that I cannot specify separate virtual hosts for mainhostname.domain.com, domain.com, or www.domain.com.
So, maybe this is all a DNS issue?