I spent some time researching hypertext pre-web, and an old idea (Vannevar Bush old) is having "trails" through your document store, each basically giving a narrative one could follow. Sun used that terminology for their Java tutorials, though it seems the nodes along the trails are unique to a particular tutorial.

I could see something like this being useful for understanding a complex and complicated document like a programming language specification. The trails would show which sections and subsections work together to produce a particular behavior users should understand.

I've also seen dependency graphs given in the preface to certain math textbooks, which is nice when you know what it is you want to know (and I wish more textbooks would be available in hypertext form).