Publishing and Non-publishing Site Templates
When planning a site structure, or hierarchy, in a SharePoint Server 2010 environment, you are faced with the decision about the site template on which to base a site collection/s and whether to mix and match site templates within a site collection, such as publishing and/or non-publishing site templates. Typically, internal SharePoint site collections include a main site collection based on one of the site collection publishing templates and then subsite templates based on desired functionality. For instance, you might have a strong need for business intelligence functionality, so your choice of templates might be based around projects.
For a discussion on SharePoint Features and publishing ...