Below is a list of key ontologies on biology and medicine

The gene ontology
The Open Biomedical Ontologies - links to about 50 ontologies ranging from anatomy to the nesting behavior of the loggerhead turtle. All ontologies are expressed in a common syntax and the list is curated.
The Foundational Model of Anatomy
the MGED (microarray) ontology consortium
cBIO the new national center for biomedical ontology - definitely a key resource

this list is not comprehensive, but it will get you started. What have I missed?

See also my bookmarks on ontology-related publications