Jakob Nielsen has written an informative entry to Alertbox this week titled, Reviving Advanced Hypertext, the column comments on some of the new features on the web today, including explicit structures, user-constructed structures (post-its), integrated browsing, searching & highlighting, overview maps (sitemaps, etc.) and physical hypertext (metaphors, real-world actions).
There is personalization, ontologies and facet classification, which fit more within Information Architecture, but play indicative roles alongside the hyperlinked structure.
In addition, the collaborative aspect that Nielsen comments on, I also feel is an area of tremendous promise in the future, including collaborative navigational structures, which engages in participation and trust.