This is quite a cool idea! We want to add more visualizations to our toolklit, and we already have a few in mind. One of them is graphs, but we never thought of using it for mapping locations, just for showing relationships. We'll add it to our list of ideas. Although for maps we would like to have something more visual than a graph representation, it could be a good first step and it opens up for many types of analysis that could be quite useful.
GraphViz is quite cool, by the way. I used it for a bit when I was doing research on social networks (as in networks of friends, not Facebook and the like). If you have big graphs and want something pretty, I would look into Gephi, which has a big focus on aesthetics. It's what I used for presentations.
And for web charting libraries, we know a few. We will probably end up using D3 or related for it's flexibility and the amount of plugins it offers, but we still have to go through an evaluation process to see what would work best for whatever we want to do at that point.
Thanks for the suggestion!