Here is a list of biomedical ontology-related repositories and tools I assembled recently for a BIRN information page. It's far from exhaustive - especially given how much ontology-related work & tools takes place outside the biomedical domain - but it's pretty thorough regarding those ontologies and tools being used by bioinformaticists.

Biomedical ontology aggregation sites:
OBO Foundry:
http://www.obofoundry.org/
BioPortal
http://www.bioontology.org/ncbo/faces/in...
EBI Ontology Lookup Service:
http://www.ebi.ac.uk/ontology-lookup/
Berkeley Gene Ontology Download Matrix
http://www.berkeleybop.org/ontologies/
NCBC Scientific Ontology Working Group
http://www.berkeleybop.org/sowg/table.cg...

Though there is considerable overlap across these sites, each provides what I've found to be invaluable non-overlapping content and/or functionality.

Specific Ontologies:
Basic Formal Ontology (BFO)
http://www.ifomis.uni-saarland.de/bfo/ho...

OBO Relations Ontology (OBO-RO)
main:
http://obofoundry.org/ro/
OBO-RO-to-BFO bridge:
http://www.obofoundry.org/cgi-bin/detail...

OBO Phenotypic Quality Ontology (PATO)
main:
http://www.obofoundry.org/cgi-bin/detail...
PATO-to-BFO bridge:
http://obofoundry.org/cgi-bin/detail.cgi...

Ontology of Biomedical Investigation
http://www.obofoundry.org/cgi-bin/detail...

Ontology Tools:
Editing/Browsing/Searching:
Protege-OWL
http://protege.stanford.edu/overview/pro...
Protege-OWL v3.3 (OWL v1.0)
http://protege.stanford.edu/download/reg...
Protege-OWL v4+ (OWL v1.1+)
http://protege.stanford.edu/download/reg...
OBO-Edit
http://oboedit.org/
SWOOP
http://code.google.com/p/swoop/
GrOWL
http://ecoinformatics.uvm.edu/technologi...

Data Annotation with ontologies
Phenote
http://www.phenote.org/

Semantic Search Engines
Swoogle
http://swoogle.umbc.edu/

Community Semantic Web and Ontology Specifications
Resource Description Format (RDF)
http://www.w3.org/TR/rdf-primer/
Web Ontology Language (OWL)
v 1.0:
http://www.w3.org/TR/2004/REC-owl-featur...
v 1.1:
http://www.webont.org/owl/1.1/

Descriptive Logic DIG Reasoners ( reason against OWL ontologies)
Pellet
http://pellet.owldl.com/
FaCT++
http://owl.man.ac.uk/factplusplus/
Racer Pro
http://www.racer-systems.com/

RDF and/or OWL Query Frameworks
SPARQL
http://www.w3.org/TR/rdf-sparql-query/
NOTE: there are a variety of systems supporting queries against RDF or OWL data, in addition to building your own means to do so with the libraries listed below. A few such systems are:

Sesame:
http://sourceforge.net/projects/sesame/
(and the related Simile Project)
http://simile.mit.edu/
KAON:
http://kaon.semanticweb.org/
BOCA:
http://ibm-slrp.sourceforge.net/2006/11/...
Joseki:
http://www.joseki.org/
Kawari:
http://kowari.org/
Oracle+RDF
http://www.oracle.com/technology/tech/se...

Programming Environments/Libraries
RDF
Jena
http://jena.sourceforge.net/
Redland
http://librdf.org/
RDFLib
http://rdflib.net/store/
IBM Integrated Ontology Development Toolkit (IODT)
http://www.alphaworks.ibm.com/tech/seman...
OWL
OWL API
http://owl.man.ac.uk/api.shtml
Pellet
http://pellet.owldl.com/

Academic Journals:
Journal of Web Semantics:
http://www.elsevier.com/wps/find/journal...
Applied Ontology
http://www.iospress.nl/loadtop/load.php?...

Meetings:
ISMB Bioontology Satellite Meeting
http://bio-ontologies.man.ac.uk/
OWLED
http://owl-workshop.man.ac.uk/
Biocurator.org
http://www.biocurator.org/