Most of you by now probably utilize Google Webmaster Tools, and if not you really should be. For those who do use Webmaster Tools, chances are you have noticed that Webmaster Tools will only recognize internal links to your site if they exactly match your setup domain. For example http://www.rapidpurple.com links will not be displayed as internal links if I have set my domain to http://rapidpurple.com. Most people think of example.com and www.example.com as the same site these days, so Google has changed it such that now, if you add either example.com or www.example.com as a site, links from both the www and non-www versions of the domain will be categorized as internal links. The same concept has been added for subdomains, so so links from cats.example.com or pets.example.com will also be categorized as internal links for www.example.com.
