Software to draw illustrative figures in papers
A free, fairly portable, and very complete tool for general illustration is Inkscape. It uses SVG as its native file format, and aside from attempting to be a decent drawing tool in its own right, one of its design goals was to provide complete coverage of the features available in SVG.

For block diagrams, flow charts, and other simple sketches of process and data flow there is Dia. It's primary design goal is to duplicate the features of Visio in free software. Like Visio, it uses a stencils and connections drawing model that works really well for diagramming relationships and flow, but gets tedious when attempting to do art.

For clean layout of directed or undirected graph diagrams, it is difficult to beat the Graphviz tools. They are primarily designed to be used from a textual description (a concise intro here (PDF)) of the graph, but there are various GUI tools that can edit their .dot files.