Mindjet MindManager is "mind mapping software". It lets users create an outline (hierarchy) that can render as a two-dimensional layout of boxes connected by lines.
MindManager's strengths are its Microsoft Office integration, its marketing, its attractive output and its corporate orientation. It comes in XP/Vista and OS X versions, the latter is a true OS X app but lacks some functionality. I've written about MindManager before; functionally it's similar to the much older Inspiration but it's a lot prettier.
MindManager has one glaring defect -- from a geek point of view. It can only do trees - strict hierarchies. No networks, no matrices, no directed acyclic graphs. No inheritance.
So a box (node) can't belong to to two or more branches (arcs).
This is a pain. Any reasonably complex domain representation needs a node to have multiple memberships.
I think the UI for this is not too hard. This is basically what a "Favorite" does in XP, or a "shortcut" does in OS X. The file lives in a single place in the file system hierarchy, but a reference can appear in another place.
Symantec More 3.1 did something similar with its outlines. You could have a branch appear in more than one place. Multiple inheritance in other words. 
MindManager could allow users to click on a box (node) and create a "favorite" that could be dragged and dropped anywhere. They don't even need to implement full references, it would be ok if clicking on a 'favorite' merely took one to the "true" object. (Symantec MORE 3.1 did the full include model.)
If some wants to displace MindManager from my desktop, all they need to do is allow me to model an acyclic graph, or even network. Trees are very 19th century.
Ok, so they have to be pretty as well.
 So it's not patentable guys. It's been done.