[waldir]

That's why I prefer outliners. They still provide the sense of an infinitely nestable hierarchy, allow focusing on arbitrary levels of it as a temporary "root" document", and allow collapsing entire trees that are irrelevant for the current work I'm doing. But crucially, if they implement live cloning of subtrees (in Workflowy, for example, these are called "mirrors"), they can also allow a more flexible graph structure as opposed to a strictly hierarchical tree.

Of course, that misses the graphical/spatial aspect of other tools, but as josephg points out, these sometimes backfire without a natural, design-encouraged way to organize the content, and a stable frame reference. I for one don't miss the ability to organize my content spatially, even though I do that when working with physical paper. I think that's because of the limitations of the medium — i.e. I spread paper sheets out on a surface, and spread content within those sheets, because it's the only way to group content in a stable manner. The nesting system performs the same function for me in outliners.