Mindmaps, with notes. Allows you to organize the information in a visual hierarchy, so that you can quickly refer back to the notes. I use Freemind[1], an open source tool.
[1] - http://freemind.sourceforge.net/wiki/index.php/Main_Page
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[1] - http://freemind.sourceforge.net/wiki/index.php/Main_Page
Some of the previous discussions about org-mode:
https://news.ycombinator.com/item?id=2423276
https://news.ycombinator.com/item?id=8668271
https://news.ycombinator.com/item?id=2091850
From org-mode website: Org mode is for keeping notes, maintaining TODO lists, planning projects, and authoring documents with a fast and effective plain-text system.