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