Haven't personally used Gnote or Tomboy, but it sounds like TiddlyWiki gives similar functionality, with the only requirement being a suitable browswer, e.g. Firefox.

One window per image is fine, but what needs to be implemented is an option where the toolbox window is brought to the front at the same time any other GIMP window is. If you are alt-tabbing or otherwise switching between GIMP and something else repeatedly, its incredibly annoying to have to keep bringing the toolbox forward because its disappeared behind another window.