In an attempt to provide more accurate link data in Webmaster Tools, Google is recategorizing links from subdomains as internal links and the www and non-www versions of a site are considered the same site. Total link counts won’t change.
As Google explained:
“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.”
Google shared this table to illustrate how the new external vs. internal link categorization works:
The big question now is whether subdomains could negatively impact the main domain and how big an influence Google's link reorganization will have on organic rankings (if any). Interestingly, HubPages split up its site into numerous subdomains in an attempt to recover traffic lost traffic from Google’s Panda update.