Here are some projects which use JGraphT (add yours here):

• The Volta project uses JGraphT for modeling control flow graphs in Java.
• http://mapmyindia.com
• Ontology example
• GrALoG - a tool to edit/visualize mathematical structures and algorithms running on them
• Cascading
• Morphoo - An object transformation framework for java
• http://www.graphclasses.org - The Information System on Graph Classes and their Inclusions (ISGCI) uses JGraphT to record the relations between graph classes.
• REWOO Scope We use JGraphT as an important part of our enterprise content management system REWOO Scope, to model dependencies created by an excel-like formula language.
• XML Boiler Automatic conversion of XML documents and its parts based on RDF data for XML namespaces
• GAMA is a modeling and simulation development environment for building spatially explicit agent-based simulations.
• Jungrapht-visualization is modernized JUNG visualization and sample code that uses JGraphT models and algorithms.
• Symja computer algebra language uses JGraphT to represent graphs and implemented functions for graph algorithms.
• pgrServer uses JGraphT as its core graph engine for routing

Maven Central allows you to explore downstream projects.

Historical:

• Aaron Harnly at Columbia University used JGraphT for role prediction based on analysis of email content and communication topology