Ontologies are shared vocabularies that are used to describe components of a particular discipline and the relationships among these components. By using ontologies, you make it easier for others (or even the future you) to understand your data. Controlled vocabularies, on the other hand, are merely lists of predefined, authorized terms.
Here are some examples of ontologies and controlled vocabularies currently in use in a variety of disciplines:
Bioportal: the portal for the U.S. National Center for Biomedical Ontology, hosted at Stanford.
Gene Ontology: a bioinformatics initiative that aims to standardize the representation of gene and gene product attributes across species and databases.
Medical Subject Headings (MeSH): a controlled vocabulary used for indexing articles for PubMed.
Chemical Entities of Biological Interest (ChEBI): an ontology of small chemical compounds.
Microarray Gene Expression Society Ontology (MGED): an ontology designed to describe microarray experiments.