Google announced on August 31st, that they would be implementing a fundamental change to the way that Google categorizes link data in Webmaster Tools.
Google’s Webmaster Tools lists links coming to your site into two separate categories internal and external. Google stated that: "Today’s update won’t change your total number of links, but will hopefully present your backlinks in a way that more closely aligns with your idea of which links are actually from your site vs. from other sites"
Prior to this change, subdomains were treated as a separate entity and any links from it would be considered as an external link by Google. As of the announcement, these will now be treated as internal links; the reasoning being that they reside within the parent domain.
Google rationalized that most users treat www and non-www domains (www.example .com & example.com) as the same thing and that many people that own a domain typical own the subdomains as well. "…so links from cats.example.com or pets.example.com will also be categorized as internal links for www.example.com".
"If you own a site that’s on a subdomain (such as googlewebmastercentral.blogspot.com) or in a subfolder (www.google.com/support/webmasters/) and don’t own the root domain, you’ll still only see links from URLs starting with that subdomain or subfolder in your internal links, and all others will be categorized as external links. We’ve made a few backend changes so that these numbers should be even more accurate for you."
Google did however give the caveat that if you own a www.example.com or example.com site, that the number of external links may appear to go down as the reclassification of the urls that were once external will now be internal, but that the total number of links (internal + external) will be remain the same.
The biggest questions that arise from these changes are: Can we speculate that Google will be changing the way they treat links from subdomains in their link algorithm? Most importantly, will fewer subdomains be listed in the SERPs as individual results?
You can read the ongoing discussion in the Webmaster World forum and the see the official Google blog release called Reorganizing Internal vs. External Backlinks