Organising thoughts and a few constraints

I am always on the lookout for a better way of visually organising a seemingly random set of thoughts and notes in order to see where there are commonalities that could be useful. Some of the tools I use include pen & paper, mindmaps, and diagrams. Some of the products include Freemind, Xmind, OneNote, and the usual selection of presentation tools.

 
Recently I found this table, via http://fluentbrain.com/ on the benefits of thinking visually, which is open to interpretation, on the benefits of using a visual tool to organise your thoughts. What stuck out to me was the reference to TOC Processes. I'm used to the idea that when you are trying to come up with a solution to a problem that there are a few constants such as Inputs, Outputs, Controls and Constraints. TOC Processes was a new term to me.
TOC Processes
TOC is the "Theory of Constraints", a term which led me to this relatively short document... "The Theory of Constraints and its Thinking Processes" from the Goldratt Institute. The document starts by relating how organisations have become measured in parts, by department, rather than as a whole entity - leading to situations where multiple parts of the same company can end up working antagonistically and as a result not performing as well as could be expected. The idea being that the TOC process can help you identify where "undesirable effects" are occuring and what needs to change - mainly assumptions that "it's always been done this way". As with most of these things there is a large element of change management which is always fun. I'm still on the lookout for the perfect note taking or visualisation tool if you have any suggestions.