Taxonomy is the science which deals with the study of identifying, grouping, and naming items according to their established natural relationships, usually in a hierarchical fashion. Nearly anything may then be classified according to some taxonomic scheme.
In a SharePoint context there are a number of items that should be planned out that have taxonomic relationships, examples (not all inclusive):
Web Site Structure Publishing Site Structure Site Navigation Managed Metadata Search Relationships Content
Following articles are good references for SharePoint Taxonomy: