You could always use Zim Desktop Wiki. Seems to be exactly the kind of thing that you're looking for, and best of all, it's multi-platform and open source.
I use it for all kinds of things. It's extremely useful. At the moment, I'm using it for my project (which features a subjective storyline... it's linear, in a way, but the story you experience isn't the literal reality of what's happening, so there are two storylines I have to manage at once). I also use it to keep track of any kind of information I collect for my project, so I have hyperlinks to Wikipedia articles, historical references, programs and resources that I'm using, credits and contributors to the project....
Really, you should try it. It sounds like the kind of thing that you're looking for. Once you get used to Zim, it's insanely handy. The main website is here
, and there's a Windows installer here