A friend brings to my attention that Emacs has an outline mode with a feature set similar to those found in Microsoft Word. This is nice to know should I ever find myself in a Linux only working environment.
Since I am in the Microsoft Windows environment, I use Microsoft OneNote for all my research information collection and mind-mapping needs. OneNote has a superset of features over and above those in Microsoft Word. It furthermore works great with recording notes using a tablet computer, allowing you to jump to the recording corresponding to various parts of your notes and (to some extent) recognizes your handwriting so your notes that searchable. It does screen capture and makes the text in these pictures searchable as well. (OneNote can technically search your audio notes also, but with much less success.) For file organization, you can even paste all your project files in a single note page.
Reference: Outline Mode [EmacsWiki]