Several years ago, I wrote a blogpost for Writer Unboxed where I described using a personal wiki to organize my novel writing process.
I currently use a separate wiki for each novel I write and use it primarily as a story bible and repository of research information. Based on Jeremy Reston's TiddlyWiki, I've tweaked the basic version to something I call TiddlyWikiWrite (TWW).
What I like about using a wiki as opposed to using a notebook or just files on my computer is that the wiki is searchable. Think a cross between a relational database and index cards.
If you want to check it out in action, I've just updated the how-to manual and the version of TWW on my website is the most current. It's free to use/alter/tweak.
The TW team is working on a complete overhaul of the core code, but it's not out of beta yet. When it is released, I'll update and let folks know.
The how-to manual is embedded below: