Theory and Publications

Graphviz Papers

Graphviz and Dynagraph - Static and Dynamic Graph Drawing Tools - a condensed overview (cite)
An open graph visualization system and its applications to software engineering - longer overview, preferred for citation (cite)
Graph Drawing by Stress Majorization - an improved algorithm for neato (cite)
Topological Fisheye Views for Visualizing Large Graphs - topological-based distorted views for large graphs
A method for drawing directed graphs - dot’s algorithm (1993) (cite)
Efficient and high quality force-directed graph drawing - sfdp’s algorithm (2005)
Improved Circular Layouts - crossing reduction and edge bundling for circular layouts (cite)
Efficient and High Quality Force-Directed Graph Drawing - the multiscale algorithm used in sfdp (cite)
Implementing a General-Purpose Edge Router - edge routing in Graphviz (cite)
Improved Force-Directed Layouts - Voronoi-based node overlap removal (cite)
GMap: Visualizing graphs and clusters as maps - displaying graphs as maps (cite)
Efficient Node Overlap Removal Using a Proximity Stress Model - Prism node overlap removal (cite)
On-line Hierarchical Graph Drawing - dynadag algorithm

Graph Drawing

Wikipedia entry. They also have a short article on Graphviz.
graphdrawing.org - annual symposia, books, data, open problems and more
Open Directory Project Graph Drawing entry.

Survey (Franz Brandenburg talk notes in Powerpoint)
Marks et al note on history of graph drawing
David Eppstein's Geometry in Action, Graph Drawing section
Graph Drawing: Algorithms for the Visualization of Graphs by Ioannis G. Tollis, Giuseppe Di Battista, Peter Eades, Roberto Tamassia
Graph Drawing Software (Mathematics and Visualization) by M. Junger, Petra Mutzel, (Symposium on Graph Drawing 2001, Vienna)
Drawing Graphs: Methods and Models by Michael Kaufmann, Dorothea Wagner
Handbook of Graph Drawing and Visualization Roberto Tamassia, ed. (On-line version)

Information Visualization

IEEE Infovis Symposia: current, past
Information Visualization Journal
FlowingData Infothestics
York U. Gallery of Visualization (see also Statistics and Statistical Graphics Resources).
Stanford University course bilbiography
Stanford University Data Journalism
Xerox PARC projects
Software Visualization at Georgia Tech</p>