Gliffy is a plug-in for confluence (wiki) and an on-line drawing tool. We use it, along with a wiki, to draw and gather UML models. Everyone on the team can edit them. No need for proprietary / desktop software.
Jim Phelps, UW-Madison
UML Modeling, CASE Tool
MagicDraw UML is a fairly heavy-weight UML modeling application and CASE tool. It is a large java application that runs on MacOS, Windows and Linux. Fairly reasonable pricing. Step learning curve. We have an Enterprise Site License though we don't use it much. Hard for beginners to use. Will save/open Visio XML documents.
Ontology Mapping Tool
Protege is being used by UC-Irvine to map their architecture(s). See their Enterprise Architecture Model and Repository
Marina Arseniev, UC-Irvine