Late in 2002 I discovered Wikis. This was perhaps a little late, but they really caught on in a big way only during the early 2000s. The Wiki Way was only published in 2001, and I was never really interested in the collaboration aspect of wikis. Rather, I liked the idea that I could have a desktop wiki for my notes. Nor did I like the idea of it being on a server (and possibly exposing my notes to the whole wide world). Wikit makes hyperlinking easy, and it does not require a server. So I first began to use it. Soon after (in May) I discovered an application called Notebook by Will Duquette, called Notebook. It must still have been version 0.9, as version 1 was released only in June of 2003. It offered everything that Wikit could do and then some.
"Notebook is a personal notebook application." It was ideal for note-taking. Even though the search function was anemic, not really allowing for Boolean searches, and even though it could not print (at least not without invoking some other applications), I loved it. But it was programmable. In fact, I taught myself the rudiments of Tcl/Tk to do some programming of my own. Notebook is available for Windows, Unix, and the Mac. the "Starkit" version is the easiest to use. It became a most interesting project for me, and it seemed for a while the solution to "the problem with index cards."
Notebook stores its pages in a flat database without any page hierarchy. The database is actually one large textfile that is loaded into memory when the program runs. This works very well. The program is fast and very reliable. And when the time came to move things from Notebook to ConnectedText, it was easy to transform Notebook's markup to that of ConnectedText with a capable text editor.
There is a very good description of Notebook in the article What is a Wiki? by Nathan Matthias. (While you are at it, you might also look at Caffeinate Your Hypertext, which includes an interesting discussion of the relation of hypertext and outlines.)
Notebook is freeware, and it is still being developed, albeit slowly. I am fond of it, but I have moved on to a much more capable application, and it now resides -- you guessed it -- on the flash drive that also contains other "old applications." What made me move to ConnectedText was not just the much more capable search function, but also the active and concerned development team. It reminds me of the early days of Ecco. And I hope that it won't be bought out ... though I am sure I would even then use it for a long time, as there is nothing that even compares - at least in my book. See also ConnectedText 3.