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[JohnnFour]

I use WikiPad for my game planning and note-taking these days.

http://www.jhorman.org/wikidPad/

30 day free trial. $12 to buy.

Once you get used to the idea of Wiki words, as opposed to tables of contents and tree views, it feels a bit liberating and becomes easy to use and reference with.

Output is to plain text files as well.