I just discovered Pencil, which seems like an interresting program, but the last update seems to be from 2008. I have the same issue with Dia.
I'm hoping that by making these projects known here, maybe other developers will contact the original developers and assist in active development.
Some of these programs are too nice to let them fizzle out.
just add to the list.

So mine are:
  • Dia
  • Pencil
  • freemind (the version in the repos is 7, while the version on their site is 9.0X Beta).