GraphML (http://graphml.graphdrawing.org/) is an XML file format for representing graphs. We support a limited set of this format (no subgraphs or hyperedges). The main constraint is that nodes need to be defined before edges (this will be fixed later on). Attribute names in keys that have the same names as those pre-defined node and edge properties above can be used to control the visual aspects of the graph. Keys with other attribute names will be used to construct additional properties for nodes and edges. Take a look at the file test.xml as a sample.
Pajek (http://vlado.fmf.uni-lj.si/pub/networks/pajek/) is a popular network visualization and analysis package. You can use GUESS to load .net files that are generated and used in Pajek. These are not fully supported, but you should be able to get most things in.
GDF, GraphML and Pajek files can be loaded from the file menu as well as using the makeFromGDF(filename), makeFromGML(filename) and makeFromPajek(filename) options.