Sharepoint: Organizing an Intranet site hierarchy

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http://serverfault.com – Not totally sure this should be here or in Stackoverflow, but I look at it not from a developers point of view but from an admins. In the past we had a pretty anemic intranet - now with SharePoint 2013 this will get a lot more use. We mostly delayed investing for the last half year ;) My problem is - how do I organize the sites so that they go best with SharePoint long term, from an admin point of view, while possibly sites get added or removed. In the past we had ONE site collection (Intranet) with sub-sites in it (not in the /sites folder) for all major parts of the small company (finance (HowTos)