InterView is an interactive tool for producing 2D layouts of network data.
It can work with simple interaction data (e.g. protein-protein interactions), but can also be used to visualize directed networks. See here for information on the data formats used.
As well as standard topology-based layouts, alternative visualisations may be produced with nodes distributed according to a distance matrix (e.g. evolutionary distances between genes) or clustered by user-defined groupings.
The resulting networks may be exported as PDF or PNG images.
You can download InterView here.