Back just about a year ago, we covered a change on how webmaster tools handles subdomains. I since forgot about that and now I see John Mueller from Google explaining it again in a Google Webmaster Help thread.
In summary, even though for ranking purposes, Google may not treat a subdomain as part of the internal main domain - Google Webmaster Tools generally does.
John Mueller said in the thread:
In Webmaster Tools we generally treat data from subdomains as being internal with regards to the domain name. With regards to creating a site structure with subdomains or sub-subdomains, we generally leave that to the webmaster :) (though as with other infinite spaces, we discourage the use of wildcard subdomains).
Just a reminder, Google Webmaster Tools and Google's algorithms may treat things different.
Forum discussion at Google Webmaster Help.

Comments:
Website Developers India
08/17/2012 12:48 pm
Thanks for sharing. I was looking for it..
Tad Miller
08/17/2012 02:36 pm
If you want to do XML site maps that you upload to WMT for sub-domains I think you need to have separate WMT accounts for them. So one account won't get it done in that respect.
Paul Edmondson
08/17/2012 03:31 pm
We don't see aggregated webmasyertools data for hubpages sub domains. Each one needs to be added and looked at individually. It would be a nice option to be able to look at the overall data easily.
Srikar Srinivasula
08/19/2012 08:00 pm
I have a question barry,i know that subdomain and main domain are treated as two different domains and thats how hubpages got out of panda on matts advice blah blah but does a sub domain carry any seo value or authority of the main domain,i mean if say i have a tech blog and i want to cover android as subdomain would that be of any advantage over a new android blog ? im really keen to know this as i am seeing a lot of subdomains on serps lately (in tech niche).
Nick Pateman
08/20/2012 08:03 am
Yes, a subdomain will benefit slightly from the main domain. How much? It's impossible to say, but no where near as much as using a subfolder i.e. domain.com/directory as opposed to directory.domain.com
Mark Hughes
08/20/2012 10:58 am
I recently had to set up a separate GWT account for a subdomain because the one thing I (don't think!) you can do is submit a sitemap if it's based within the subdomain. Otherwise, it makes total sense in most cases to treat subdomains as internal pages.
Guest
08/20/2012 06:40 pm
@Barry, To what do you think he is referring when he said "we discourage the use of wildcard subdomains"? Thanks, Russ
Russ Offord
08/20/2012 06:41 pm
@Barry, To what do you think he is referring when he said "we discourage the use of wildcard subdomains"? Thanks, Russ
Steve Duffy
05/15/2013 09:21 pm
Agreed. I have a site that uses multiple subdomains for geo-location (e.g., sandiego.domain.com vs. houston.domain.com) and each one has to be looked at individually. I would *love* to be able to aggregate this data. The only upside is that Google Analytics supports a global approach to subdomains, so while you can't easily see rankings, you can at least attribute traffic.