Portal and site taxonomy is very important because it greatly influences the usability characteristics of the portal/sites. The term "taxonomy" is usually associated with a system of classification and/or a way of organizing things. So in a portal or web site, taxonomy is typically the organization of the content such as pages and documents. Usually, the navigation system is tied in part or in whole to the taxonomy.
SharePoint (or for that matter any portal software product) does not include a usable pre-built taxonomy. This work is left up to the users because it is highly dependent on industry and company business characteristics.
Usually, the best way to develop a taxonomy is to organize a cross-functional team of users that will work together to design an organization of topics or subjects that are meaningful to the organization as a whole. A technique referred to as "card-sorting" is a frequently-used method of working through a taxonomy design project. You can read about it here:
http://www.infodesign.com.au/usabilityresources/cardsorting
In some cases, organizations are so large and complex that they need assistance from a specialist to develop a good taxonomy. There are a number of consulting firms in the U.S. that are very good at this sort of work such as Project Performance Corporation in Washington, D.C.
http://www.ppc.com/Pages/default.aspx
