Gephi the open graph Viz platform
DBMS supporting graph, document, full-text and geospatial models
A premier mind-mapping software written in Java
High-speed, 3D-friendly, TightVNC-compatible remote desktop software
Optical Design Software for simulating systems of lenses, prisms, etc.
Syntax Tree Drawing Software (Linguistics)
A Tool for Control Structure Selection in Interconnected Processes
UNIX Performance Monitoring / Trend Analysis Java Software
Free data acquisition and data visualization cross-platform software
Java-based scientific graphics
A tool for visualization and analysis of logs as sequence diagrams
jchart2d is a real-time charting library written in java.
The most popular mindmapping and brainstorming software
Live Trace Visualization for Large Software Landscapes
Portable Ubuntu Linux for Scientific Computing
Build digital chronogram quickly and easily
Java software for building a 3D model for FEM Analysis.