The site I'm about to mention will be most appealing to you if you use Macs, and more worthwhile still if you're either able to read French or in the mood to cope with online translations.
If you're still with me, let me recommend a site from the French media figure and academic Dominique Renauld, who has put together a number of tips, tutorials, and analyses of how he uses computerized thinking-and-writing tools. These include the nice diagram of his flux de travail, or workflow, shown in the image above and elaborated here.
As the icons in that image suggest, M. Renauld makes extensive use of two programs I also find elegantly effective and have often praised here: Scrivener, and Tinderbox. You can find the section of his journal dealing with "writing tools" here, with tags for Tinderbox-related and Scrivener-related posts. He has also prepared how-to videos on, for instance, using Tinderbox for organizing research notes via tagging. Others are here, with a sample below.
If this is the kind of thing you are interested in, you will find it very interesting.
Thanks to Dominique Renauld for the effort and ideas.
Update: A very interesting four-year-old video by a man named Tom Webster, about categorizing information with a now-quaint version of Tinderbox, is available here. Today's version can do a lot more, but this gives you some ideas.