Incorporate the possibility of layers.

E.g. the same root node could have different children on different layers. [They could remain visible by having different levels of transparency (probably a max of 3 layers for clarity here?)] Thus the same root node could be explored in different contexts represented by the layers themselves.

One example (obviously users can create their own use-metaphors) might be that the root node represents a 'cause' with child nodes representing 'effects'. Different layers could show the effects of the root node "cause", given differing contexts- i.e. the cause has different effects in differing environments. However - effects common to different environments could colocate spatially so that you could easily see correspondencies and relationships.

Another application might be website mapping - relationships between pages in one section could exist on one level, whilst resources common to several levels (ie pages linked from several sections) might colocate over several layers.

All of which is to say that the visual metaphor of co-location is possible over layers: "something stays the same while other things change" - "something remains necessary whilst all around it differs", "something keeps occuring even when the circumstances have changed".

The possibility for confusion and obfuscation is of course a danger here, but used carefully, it might add something to the analysis of and integration of ideas.