I am working in the NDepend team and we switched from GraphViz to MsAgl (Microsoft Automatic Graph Layout) in september 2008. The MsAgl license allows commercial utilisation. Here are a few sample pictures of MsAgl graphs integrated in NDepend (everything is interactive, nodes are movable/selectable/removable/clickable, edges are editable/selectable/removable/clickable, the layout is zoomable, and also, while it could be cleaner the MsAgl API is clean enough to work with):
