i use yEd from yWorks for all my diagramming.
it is based on GraphML, can import nodes/vertices from excel/XML, it has good automatic layouts for large diagrams, and can output to GraphML, SVG, JPG, and many other formats.
yEd and GraphML is very versatile indeed. Years ago I worked on a quite big mobile game project, we used graphML to be the main quest / level / story format of the game and naturally yEd was the editor of choice. Pretty scrappy but it worked, somehow.
