A few days ago, I've cobbled together a note-taking solution for my email messages. It's very unixy, consisting of a fair number of different parts working together: Claws Mail with the Python plugin and two of the shipped example scripts on the one side, Tomboy with the Claws Mail addin and the Reminder addin on the other side.
Starting with a message selection in Claws Mail,
a click on the "Create Tomboy Note" menu item of the Python example script results in this dialog popping up (I know that this dialog is ultra-ugly, but hey, it's a quick&dirty easy-code example script, nothing more)
which in turn creates this Tomboy note
The Tomboy reminder plugin will take care to remind me about this next monday by raising the note.
To make the round-trip complete, there's a second example script that raises all Tomboy notes that link to a selected message.
Okay, admittedly not the end-user friendliest setup, but it suits my needs pretty well. And it shows the benefits of scripting language interfaces for glueing components together -- it didn't take long to write the scripts to make this work, even though the plugins and addins have not especially been designed for it.