NoteLynX Pro combines an outliner, a graphical tree view, and interlinked notes. The feature that distinguishes it is that a single note may have more than one parent.
That sounds like a detail and it changes the data model entirely, because a note with one parent is a tree and a note with several is a graph. The practical problem it solves is one every hierarchical note system eventually hits, which is that real information belongs in more than one place at once, and a note about a supplier belongs under both the project and the vendor without either being the true location. The usual workaround is duplication, which then diverges, or tagging, which is a second parallel system to maintain. Allowing multiple parents means the note exists once and is reachable from every context it belongs to, and the tree view renders that honestly rather than pretending there is a single path to it. On top of that structure sit wiki style links inside note text and explicit links in the tree view, which is a second way of relating notes that is associative rather than structural, so a reference can be made without implying that one note contains another.
The flexibility is also the difficulty, since a graph is harder to keep tidy than a tree and it is possible to build something nobody can navigate. It rewards a person who thinks about structure and frustrates one who wants to write and move on.