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:
Can you talk about how you treat sub domains? We have 5. Similar topics but different enough we would have put them in separate folders. Instead we used subdomains. Does this hurt us in the rankings?
No, not in general.
So we recognize that some sites use subdomains as different parts of the site. And, in the same way that other sites might use sub directories.
With subdomains, the main thing I'd watch out for is that you're not using wildcard subdomains because that can make crawling really, really hard. If we have to go through all of these subdomains and treat them all as separate hosts.
But if you have a limited number of subdomains then that might be an option.
Similarly, if you have different sites that are essentially completely separate websites but they're in subdirectories-- so in folders-- then we'll try to figure that out as well. And say, well, actually these are all on the same domain, on the same host name, but these are maybe user-generated content-- like separate sites that should be treated completely separately-- then we'll try to figure that out as well.
So that's not something that would kind of like improve or hurt rankings. It's more a matter of us figuring that out. And so far I've seen our algorithms do a pretty good job of that.
Here is the video embed:
So I guess Google is typically smart enough to know how to treat your subdomains and subdirectories.
Forum discussion at Google+.