The SEO debate on using subdomains and subdirectories is one of those things that will never die. But Google’s John Mueller said in a Google Hangout on Google+ the other day that it really doesn’t matter that much. He said Google does a pretty good job figuring out what you are trying to do and it doesn’t matter that much.
He said unless you have massive numbers of wildcard subdomains, you should be fine.
He said this at the 48:24 mark into the video:
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So I guess Google is typically smart enough to know how to treat your subdomains and subdirectories.
Forum discussion at Google+.