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 Extensions Journal + Todo + Tags can lead to a very effective Tasks Manager
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 No mobile app support
This is a desktop app and there are no mobile versions available. This can make it more difficult to use on-the-go if using cloud storage to store files from the app, as there is no mobile app version to access those files.
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.