dot and friends are great for small graphs, but the tools break down horribly on larger data sets. It's especially hard, for example, to get a graph where the edges don't cut over nodes (making the nodes unreadable). Even Visio has issues with this...Second, for those of you working with graphs, graphViz.org has an awesome graph visualization tool that we use for research. It has a very simple syntax and lots of examples.
Various output formats also fail for unknown reasons. (The image outputters, such as .png, work reasonably well - it's other ones like .pdf that break easily.)
dot has a slight advantage over Visio in that it runs everywhere and its format is dead-simple.
