The Google Webmaster Blog announced a significantly large change to how Google Webmaster Tools classifies subdomains.
Prior, subdomains would be considered separate sites and thus a link from a subdomain would be considered an external link by Google, in Google's reports. Today, Google is changing that and now considering those links internal links.
So when I link from forums.seroundtable.com to www.seroundtable.com, that is no longer a link from an external domain, it is a link from an internal domain.
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.
Here is the table they used to explain it:
|Links for www.google.com||External links||Internal links|
|Previously categorized as...||www.example.com/|
|Now categorized as...||www.example.com/|
So does this impact how Google treats links from subdomains in their link algorithm? I think so. Hubpages played on it and said it helped with Panda.
Does this mean that Google will list less of your subdomains in the search results as individual results? Well, yea - they have already with the new mega sitelinks, which interestingly doesn't apply for a search for [google].
In any event, keep note of this significant change, not only to the reports within Google Webmaster Tools but to how it defines the search results, linking algorithms and so on.
Forum discussion at WebmasterWorld.
Update: Google has clarification that this does not impact rankings. See more details over here.