Google has changed the way they handle reporting links within Google Webmaster Tools. Instead of considering subdomain links as external links, they are now considered internal links.
Google made this announcement on their Google Webmaster Blog, explaining that this applies to both the non-WWW and WWW versions and other subdomains on the domain name. Google said:
Most people think of example.com and www.example.com as the same site these days, so we�re changing 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. We�ve also extended this idea to include other subdomains, since many people who own a domain also own its subdomains�so links from cats.example.com or pets.example.com will also be categorized as internal links for www.example.com.You should notice a change in how the links are categorized within Google Webmaster Tools link reports.
But what does this mean for how Google handles listing subdomains in the Google search results and how Google’s link algorithm treats links from subdomains off your domain? That is unclear from the blog post, at this point.
In 2007, Google changed how they handled subdomains by indenting more but that flipped back and forth over the years. With the new 12 sitelink pack, less results from the same domain, and subdomains will take up indent listings in Google, instead they will be grouped in the Sitelinks pack.
On the algorithm side, on how Google handles link weighting for links from subdomains of your site, we have no idea yet. Google has not said anything to my knowledge on that matter.
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