One strategy for doing this is to offer the expert version as the primary page, with links to clarifications of difficult points. Another use is to try to involve the reader more deeply in a story by offering different storylines the reader can select. This genre has its own design conventions, as in this HTML-ized version of a story by Kibo and this cgi version of the original Colossal Cave adventure . And another by Gareth Rees that covers the same ground with nicer examples, and a good bibliography with live links, at the end. Yet another use for hypertext is to allow parallel reading of two texts, especially a 'classic' alongside a commentary or a set of annotations.
Wake are two examples.
I think this problem requires the most delicate attack, because the text being annotated will be trying to establish its own continuity and rhythms, and peripheral material is bound to disrupt these. Yet another use of hypertext is to add a dramatic element of suspense . This book ad does a nice job of this.