Recs.
Updated
Zim is a desktop note taking app that allows the user to form wiki like structure with the notes contained within. A Windows and Linux client are available.
SpecsUpdate
Pros
Pro Basic formatting is fast and just enough
Apply H1,H2, H3, bullet, numbered or checkbox list or bold, italic, highlight and code snippet with a simple shortcut. (No more, we don't want to go the MsWord way do we?)
All these are recognizable in the source file and can be edited by any text editor.
Pro Plain text data format rather than proprietary
If/when the app is no longer developed, or if the user decides to no longer use the application or view/edit them on a non-supported platform, it can be done with any plain-text editor.
Pro Allows for organized, wiki-style navigation
Notes can contain links to other notes, allowing you to reference important information when needed. This way the user can connect and reference many different pages in the app, keeping things clean and structured, unlike Evernote, which makes this a good Evernote alternative.
Cons
Con Wiki formatting instead of Markdown
The tool's formatting uses a docuwiki style format, which is similar but not quite markdown. It would great if it was markdown instead, making all its content far more easily useful to other tools too.
Con No native sync support
Zim notes don't automatically synchronize with other devices or offer built-in cloud sync support. Of course the user can add the files to Dropbox, or something similar, to then open them on another device with the app installed. But this is more of a work-around than a built-in solution.
Con The Pro that it's a pure Wiki is also the con: inserting rich content can feel very 1980s
Con Can be difficult to install
There is no pre-packaged solution for installing Zim on OS x, though the user can build from source if they like, this just may be more difficult for a casual user.