I do as well. But I end up still needing a white board to map out all the various dependencies etc in my project. Thoughtwriter doesn't seem to have the option to write freeform (not line by line) but if they add that, this could be super useful.
For freeform stuff (usually website mockups), I'll usually just grab a piece of paper or use Inkscape.
Inkscape is probably a decent tool for thinking (at least if you're already familiar with it), since you can zoom in and out on an infinite canvas, draw and type things, etc.
Thanks for sharing. Perhaps it's better to make the free version have more (all?) the features, and then charge for having more than one drawing. It's a bit hard to commit to paying for a service before I've been able to use it successfully. A pro account is required to move items around, for instance, which makes it difficult to see what it would be like to use the full version of the tool.
