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TreePad Plus ($30, 21-day free trial) is a truly venerable program, born in the age of 56.6K modems and pundits declaring the Internet a passing fad. Unlike those modems and pronouncements, however, TreePad Plus is still alive and actively supported. It continues to be a leading tool for organizing any kind of information that lends itself to being turned into chunks smaller than a novel and larger than a database row.
TreePad Plus uses a familiar "Outline and Detail" view. (The author's claim to have originated this model is somewhat suspect, since it was a common metaphor on the Macintosh years before TreePad 1.0.) The left-hand pane shows topics and sub-topics, nested as deeply as you may need. You can apply icons to topics, or to an entire subtree, so you can visually "flag" some topics. The right-hand pane shows the data in a topic, which can be simple text or a full-featured document with varying fonts, alignments, shadings, and line spacing. Tables can be inserted with considerable functionality, including merging/splitting cells, styled text in each cell, and so on. Perhaps most important for functionality, each article can contain clickable hyperlinks--to other articles in the tree (including to "anchors" in articles, so you can jump directly to the part you need in a long piece of text), to web pages, and to disk files.
TreePad Plus can also import data. While many programs will import a single text document as an article, Treepad Plus will also allow you to import an entire directory into a subtree, with each document (text, RTF, or HTML) becoming an article, even recursing down the tree if needed.
TreePad Lite, the freeware version, offers far fewer features. It has the tree and the text, with extremely limited formatting, search, and linking options.
If TreePad Plus has a flaw, it's that the program is visibly weighed down with features. Each iteration of functionality adds more menu items, icons, and buttons. Interface metaphors which were state-of-the-art when the "blink" tag was cutting edge are being overloaded with more functionality than they can clearly convey to the user. In Treepad Plus's defense, a program doesn't remain actively supported for more than a decade without building a solid and loyal user base--and switching to a more modern interface, no matter how much might be gained, is likely to annoy those who have stuck with it for so long.
Over the past decade, I've used two text information programs daily for personal projects: ConnectedText ($40) and TreePad Plus. The particular type of information I work with is marginally better served by Connected Text, but I have no hesitation in recommending TreePad Plus for most user's needs--even if booting it up does give you flashbacks to the era of Pets.com.