When I need a tool to organize things with a graph I usually just use yEd. You c...

When I need a tool to organize things with a graph I usually just use yEd. You can do a surprising number of things with it:

- Graph layout algorithms

- Graph scoring (centrality etc.)

- Variety of node types

- You can add custom node types (to a point), even use pictures of things

- Cross-platform (not open source sadly)

- Swim-lanes, grids, grouping structures

- Graphs are saved as .graphml xml

and so on. It's not perfect, I wish I could also just drop in multi-media type files and turn them into node representations.