[GianFabien]

I'm still looking for a software design tool that doesn't suck.

In the meantime, I simply use pen, paper and ring-binder. I tend to write with the granularity of a single page. That is, decompose functionality, etc, so that resulting sketches, etc fit on a single page. I don't fear mostly blank pages. Easier to find stuff as I flip through the pages.

Once I get down to the granularity of a class, function, module, I implement it and mark the page as done with a date. Any key design decisions, discoveries, etc are transcribed into the comments of that source file.

I also use GraphViz to generate some dependency diagrams. SVG files are easy to view with any HTML browser.