Wiki Way
One of the most surprising aspects of The Wiki Way (by Bo Leuf and Ward Cunnigham) is its emphasis on Wiki as a personal notebook.
Wiki makes a great tool for storing notes, but it's not really a wonderful tool for making them. You need to write in a browser, which is a nuisance -- and, for personal use, Wiki's write-anywhere ubiquity doesn't do you much good. Tinderbox is probably a better answer. (In fairness, Wiki runs on lots more platforms, and Tinderbox didn't exist when the book appeared last year)
We now have round-trip Wiki editing running in a beta Tinderbox environment. You download a wiki and drop it into Tinderbox, edit what you like, and then export the changes. Mirror the changed files, and you're set. The prototype Tinderbox follows WikiStyleLinks, so you have Wiki links as well as conventional Tinderbox links. (More in Books...)