I think it is telling that most of the tools on this website (and in similar collections I have seen) are diagrammatic in nature. Diagrams might have been the most important “tools for thought” since our ancestors invented lists, tables, calendars and maps, long before recent note-taking app startups used this expression for their marketing purposes (which is absolutely fair and I am always happy to see when thinking tools become more popular outside of business/science contexts).

I think it has something to do with how intertwined structure is with diagrammatic representation. Models as well as systems are all about structure, which is why you often see them represented in diagrams (and if you don’t, you may still think about them in diagrammatic terms). And yet, historically diagrams have often been neglected in science until very recently.

I believe digital tools are still missing a lot of their potential as thinking tools because of how text-centric they are. I don’t suggest that it could have been different, given technical constraints and demands, but maybe computers would aid our thinking much more if they would actually allow us to more freely and intelligently draw diagrams. Ivan Sutherlands Sketchpad was a great step in that direction (I am sure most of you have seen it: https://en.wikipedia.org/wiki/Sketchpad) and more recently the work of Bret Victor (http://worrydream.com/MediaForThinkingTheUnthinkable/). But in many regards I believe that paper is still superior to what we have done so far.

Obsidian.md is a pillar in the modern "Tools for Thought" space (along with logseq and Roam Research). Obsidian's plugin ecosystem is enormous, and features robust, bidirectional integration with Excalidraw. Notes in your diagrams, diagrams in your notes... combining text and visual/spatial sketch and whiteboard tools is profoundly powerful.

https://github.com/zsviczian/obsidian-excalidraw-plugin

Now there's also ExcaliBrain which builds on Obsidian's graph view:

https://github.com/zsviczian/excalibrain