[TommyW]

But on the desktop only.....

That I'd use for this, two other pieces of software. The first is VoodooPad, a freeform, as structured as you wish, wiki generator, it's great. There's a free version and two paid versions. It's got good export to HTML and there's a bunch of plugins. It's got an active user base with lots of scripts and a cool developer too.

Second and perhaps directly structured along what you say is MacJournal, which is diary/blogging software. You can have multiple journals each with multiple entries, all sorted by date with wiki style links between them. It supports export to HTML and works with all the blogging services out there. If you're a writer you'll enjoy the full screen mode.