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Tomboy meets Leaftag.

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And finally, after convincing gnome-open to use Tomboy to open note:// URIs, selecting the entry in the Deskbar menu will open up the freshly-tagged note.

Yeah, it's bit of a hack, but it's a start.

You need Leaftag (the latest version from SVN plus, at least at the moment, a patch for libleaftag-gtk), .NET bindings for leaftag (no tarballs yet but a mirror of my darcs repo is available) and the Tomboy plugin (again, there's a darcs mirror.)