VoodooPad is a desktop wiki, recommended to me by a cow orker. It's made by Flying Meat, who describe it as a "garden for your thoughts." Some folks thoughts are ticker-tapes, others slag heaps, I like a garden.
I'm trying to replace the myriad Stickies on my desktop with a "notebook" type of app and this is the best I've seen so far. It's easy to get started by copying and pasting old notes into it ... and it's just as easy to go the next step to full wiki-style linking and templating and categorizing madness.
VoodooPad includes a plugin framework and comes standard with things like word count, alphabetize and record audio. You can even insert quick sketches that you draw right on a page using your mouse.
It's awesome! And free to download and try out. $29.95 removes the fifteen-page limit imposed on the free trial.