Many (but not all) use GML as a data format.
- good to have SVG view?
Mind Mapping is a subset.
Piddle is is a Python module for creating two-dimensional graphics in a manner that is both cross-platform and cross-media; that is, it can support screen graphics (e.g. Quick Draw, Windows, Tk) as well as file output (PostScript, PDF, GIF, etc.).
Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other Python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library.
Mathematica and its clones
- looks like a Flash app, but does have export of JPEG/PNG/SVG
- hey, it actually does connecting vectors that move with either end! (Unfortunately they're right-angled, not pretty curves.)
TouchGraph: for rendering, not editing
- what does The Brain use for WebApp? It's not Flash (in Feb'2013)
- http://raphaeljs.com/ SVG
- ProtoVis http://mbostock.github.com/protovis/
- CoffeePhysics http://badassjs.com/post/18503583619/coffeephysics-a-fast-new-physics-engine-written-in
- http://bl.ocks.org/rkirsling/5001347 editor
- Software Galaxies code-dependencies viewer https://github.com/anvaka/pm/tree/master/about#software-galaxies-documentation
See also manual diagram tools.