I write until thoughts stop coming to mind. It often takes a few hours, but it is really therapeutic. I mind-dump everything that I think of, without editing or stopping. Usually, the topic ends up centering in on the place where I have the most amount of uncertainty. It often gets pretty meta, which actually does tend to be helpful.

I find that getting recurring thoughts on paper (into a text editor) can make them feel 'handled'. The mechanism for this is basically mysterious to me, but it came from GTD.

Another idea is to dedicate time in your day to worrying. Set aside 20 minutes to do nothing but worry. I haven't tried it, but I've heard good things.