Taxonomy is the practice and science of classification. SharePoint taxonomy, In additon to Managed MetaData it includes how sites are organized, content is arranged, menu's are laid out, etc.
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: