In the context of web pages,the doctype declaration refers to a Document Type Definition (DTD). The DTD specifies the rules for the markup language, so that the browsers can render the content follows the rules of that markup language i.e. different versions of the doctype render content in different ways.
In early versions of DotNetNuke the doctype was a fixed part of default.aspx and was set to "HTML 4.0 Transitional" which was not ideal for sites wanting to create valid XHTML markup. With 4.4, the declaration has been made dynamic, to allow users to declare particular doctypes with particular skins.