Lion Server: If I create two websites with the same domain name but different ports, web service won't start
The creation of __shadow.conf files might not be stopped in Lion Server.

Apache can be stopped from loading these __shadow.conf configuration files by modifying /etc/apache2/httpd.conf. 

There is a section at the bottom that looks like:

&lt;IfDefine WEBSERVICE_ON&gt;
    Include /etc/apache2/sites/*.conf
&lt;/IfDefine&gt;


You could change that to for eample (expand the list to match all tld's that your are hosting):

&lt;IfDefine WEBSERVICE_ON&gt;
    Include /etc/apache2/sites/virtual_host_global.conf
    Include /etc/apache2/sites/*_.conf
    Include /etc/apache2/sites/*.nl.conf
    Include /etc/apache2/sites/*.com.conf
&lt;/IfDefine&gt;