I find mind maps to be an excellent way working. I've tried wikis, org mode, plain text files. The mind map is fastest way of tidying up a mess for me and I found I usually don't have time for doing much more. It's either that or a text file. I'm just not going to put in any more work despite my good intentions. If I need to publish something then of course I will put it in a document.

If I'm learning about something or just debugging or designing then I'll use the mind map like a text file. I just type a paragraph and hit return. Each paragraph is a node but initially it's structurally no different than a text file - a list of paragraphs. The big advantage is that later I can take some of those nodes and put them under a sub-node. Its a great filtering tool, (filtering in the sense of signal to noise reduction). Maybe it's just because I am naturally so disorganised that I like it. Stuff comes out of my mind unstructured. I need a refactoring tool and I want one that's as lazy/easy as possible.

Some kind of an org-mode tool can work ok but I found it to be too slow to create links and embed images. Wikis are just too painful. At least in a mind map what you see is what you get and in fact the structure is right in your face (a bit like lisp).