Check the full post for more on hypertext personal information management tools
Over the decades I've often written about "interesting" programs, or "software for thinking," from Lotus Agenda (also here) or Lotus Magellan in the olden days to Zoot (about to come out in a new version) or InfoSelect, to Chandler or bCisive (also here) or ThinkingRock or PersonalBrain or NoteShare now. Among others.
One of my current favorites is (Mac-only) Tinderbox, whose creator, Mark Bernstein, was a guest blogger in this space recently.
Steve Zeoli, of Vermont, has an extensive posting about Tinderbox at Mac Appstorm that is a model of how to both assess and explain a complicated piece of software.