The NSM (Non/New Season Manager) system is best for saving and recalling the state of the graph. RaySession is a modern NSM front-end+backend.
There's also LV2; it uses RDF to define both the audio unit properties and the relations between them. If only Ingen and mod-host and Carla, with their LV2 plugin graphs, went the full hog and could be used in their (Ingen and Carla anyway) LV2 plugin forms to work as easy-to-make semi-modular software synths, that would be cool. (Part of the thought behind LV2 was to provide a session/graph saving format)