INFO VISUALIZATION: Edward Tufte has posted a draft chapter of his forthcoming book. It appears to cover displaying graphs (as in the graph theory sense of the word -- think vertices and edges, not as in meaning "charts," as is often colloquially used).
Here is a complete draft of a chapter on linking lines and causal arrows from my Beautiful Evidence.
This chapter suggests methods for showing linking lines and causal arrows, and also demonstrates ideas for assessing the credibility of various links. That is, the links themselves are taken as explanatory evidence.
I haven't had a chance to read it yet, but will spend some time with it this afternoon. If there was one thing I learned in data structures class, it was that graphs are awesome and kind of fun in a perverse sort of geek way, but hard to display in a clear and intuitive way.
Oh, and Steve Tanimoto is awesome too. The best CS instructor I've ever had.