I thought it might help to have a writing tool that would let me note the questions as they came up and return to address them later. So i whipped up a "question wiki" — just like a wiki, except that the title of each page is a question. The restricted form prevents it from doing what most wikis naturally do (it doesn't lend itself to putting lots of little hyperlinks inline), but it seems to lead to an interesting and different style of use. The nice thing about using questions is that they prompt me to answer them — there's almost always an obvious thing to be written next, which helps keep the thoughts and words flowing.
I'm still mucking around with it, but here's a sandbox for you to play around in so you can get the idea. To link to a question, just begin a new line with "->". The question pages are automatically numbered so that if you change the title of a page, the title will be updated everywhere.
I'm finding that it works not too badly as a thing for me to think in. I have no idea how well it would work as a shared multi-user tool. It might be an interesting way of maintaining a FAQ, though.