A few suggestions that are in related veins are MS OneNote (included with most Office bundles), various Wiki software, and my favorite, DEVONthink. Each of them allow you to store bits of information in separate packs, while linking to and from other bits of information. I believe OneNote even allows you to put together image maps so you can link from the image to bits of info. I believe Evernote is in the same universe, but I haven't used it. This is what I do. DEVONthink lets me do wiki-style links between items, and it has a pretty sophisticated "See Also" feature that uses an AI engine to guess that other notes are related. I've heard rave reviews from GMs who use OneNote, and a lot of people use the wikis available standalone or in sites like Obsidian Portal to good effect. The main value in this kind of system is that you can hook from any note to any other note, rather than being a straight top-down method.

Another type of option is outlining software. MS Word does this of course, but there are also dedicated outlining tools like OmniOutliner. If you think well in hierarchal outline fashion, this can be a good way of doing it.