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This is why they were so easily used as a spam technique several years ago: The SE's saw them as different sites, so links between them were counted as IBL's from external sites. But of course the site owner had full control of all those links. This problem has been addressed by the SE's for the most part.
Didn't mean to imply that you were. ;-)
I brought it up partly just because it's closely related to your question, and partly because after the technique was very abused, I think that the SE's now red flag these situations as potential spam, especially when the content between the sub's is closely related...e.g. geo variations of the same topic, etc.
Not saying you should avoid them. There's nothing about subdomains that is necessarily bad. I'm just suggesting that you might want to be careful how you use them so that your site(s) don't look like spam to the SE's.