JGraph is a free, mature, and robust Java diagramming library. It contains all the graph visualization, layout, and interaction functionality you might expect in a graph library, including multiple views, layering, zoom, drag and drop, undo, automatic expanding and collapsing, routing, and layouts. You can create workflow editors, BPMN, CAD tools, network diagrams, database visualization tools, and more. It is fully documented, including examples, and has an active support community.
jTracer is a visualization tool for libcsdbg. When libcsdbg creates a stack trace for a caught exception, a thread, or a process-wide stack trace dump, it can be configured to broadcast the trace data through TCP/IP (UDP/IP, RS-232, USB, etc. are under development). jTracer catches those data and visualizes them to the user, sorted and ordered by TCP/UDP/IP address/port (or serial port), process ID, and executable, thread, and timestamp. It's particularly useful when you're doing cross-development and your target platform has no resources to visualize output. The rationale behind the development of jTracer is similar to gdb/gdbserver functionality.
SCaVis is an environment for scientific computation, data analysis, and data visualization designed for scientists, engineers, and students. The program can be used for function and data plotting in 2D and 3D, histograms, statistical analysis, and symbolic calculations using the Matlab/Octave high-level interpreted language.
EtherApe is a GNOME/pcap-based etherman, interman, and "tcpman" clone. It displays network activity graphically. Active hosts are shown as circles of varying size, and traffic among them is shown as lines of varying width. It supports Ethernet, FDDI, Token Ring, ISDN, PPP, WLAN, and SLIP transports. It knows about VLANs, IP, IPv6, TCP, UDP, FTP, and a number of other protocols. Additional statistics windows will let you concentrate on protocols or nodes.
JGraphpad Pro is a complete application framework for rapid development of JGraph tools. It is meant for developers who wish to provide a stand-alone, rich-client graph application. The user interface is configurable with XML, and it uses a plugin architecture for extra functionality. It features a wide range of application components like palette, overview, the ability to export to many image and XML formats, copy and paste, drag and drop, rich text labels, database or backend connectivity, and visual complexity management. You can use it to create workflow editors, call graphs, CAD tools, network diagrams, database visualization tools, and more.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.