I use a tool called Zim Desktop WikiZim Desktop Wiki. I guess it is similar to the already mentioned Tiddly Wiki, but I like it because it is damn fast even with a large database, flexible, linkable, and it saves it's data in .txt files which can be read and editet easily while still being able to attach pictures, maps, and other files there.
If I have pdfs I can attach them to one document in the wiki and open it from there, I also entered most data for the systems I am using (Labyrinth Lord and Traveller) and now can pull up any info I need (hmm... Stirges have what stats?) with a few mouseclicks.
I can edit all the documents on a fly and it saves automatically whenever I move away from the field. Hmm, I actually do most of my writing in this tool by now.
Finally one of the neatest things about it is the possible use of hyperlinks. When I write a scenario I do not have to copy all the info that might or might not come up into it, I can just drop a link to another document in there and if it comes up during play I can navigate there. http://zim-wiki.org/
