[kryten]

Pencil + paper.

Then zap it with my DSLR. Or if it needs to be published, use Dia and export SVG/png into target document.

I occasionally write out graphviz stuff from my code using a very light weight library I wrote (C struct to stdout) if I'm trying to visualise what is in memory at a point in time. This has been invaluable whilst knocking up a simple mark-sweep GC for a project I was working on.