Stephan pointed me in the direction of SnipGraph, which looks lovely. Essentially it takes wiki style plain text, and creates graphs with layout. It can run independently of snipsnap (i.e. on its own, in a build), to produce many pretty views of the structure/relationships you might want to model.
It's all produced by a very clever lady called Elka Ehret.
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Other similar tools here and here
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