[spodek]

A game-changing tool for thinking for me is mindmapping software. I recommend Freeplane https://en.wikipedia.org/wiki/Freeplane, released under a free license available on most operating systems.

It simplifies and clarifies without burden, enabling you to think about your work.

[pugio]

Does it support (or are there any others you've encountered that support) non-hierarchical links? A severe limitation of most mind-mapping software is that every node needs to be in its own little slot in the hierarchy; I don't think like this. I think in graphs, and interrelations – I suspect most people do. If I can't connect widely spaced nodes with some kind of edge, it's not a map of the mind at all.

[loopbit]

Exactly my issue with all mind mapping apps I've tried - they are trees, not graphs, and I don't think that way.

I find them useful for to-do lists, but little else. Even if you can connect two separate nodes, the tool doesn't use that new information to change the organization of the nodes (something like a force-directed graph could be interesting).

[tonyarkles]

https://www.literatureandlatte.com/scapple/overview

Scapple just lets you draw nodes and edges. I fell in love with it a while ago and use it to collect my thoughts, and to put together project plans (treating it like a dependency tree, even though it doesn't impose that constraint on you)

[Tylast]

Agreed. I've been liking The Brain for it's treeless approach. http://www.thebrain.com/

[dhimes]

Is it superior to pen(cil) and paper?

[stinky613]

Superior would be tough to justify outright; but it's certainly nice to be able to CTRL+F