Cytoscape is an open source software platform for visualizing complex-networks and integrating these with any type of attribute data. A lot of plugins are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
Visualizing.org is a community of creative people working to make sense of complex issues through data and design… and it’s a shared space and free resource to help you achieve this goal.
Graphopt is a graph layout tool that was created by Michael Schmuhl for graphs that other layout tools (Graphviz, for example) could not produce meaningful visual representations.
Gephi is an interactive visualization and exploration platform for all kinds of networks and complex systems, dynamic and hierarchical graphs.
This started with the simple question "how exactly does package X pull in package Y when I install it". The only way I knew of was to use aptitude interactively and just guess which package was the most likely culprit.
An animation showing edits to the OpenStreetMap.org project during 2008.
