TVi ("tree viewer with interactions") is a tool for the visualisation of network data in the context of a phylogenetic tree.
See here for information on the data formats used.
Networks are represented on the tree using either arcs between terminal nodes or as an interaction matrix.
The resulting networks may be exported as PDF or PNG images.
You can download TVi here.
Update 8/4/08: v1.01 of TVi is now available, which handles networks of up to 2000 nodes.