One feature that is missing in all versions of the Mozilla Thunderbird desktop email client is the ability to take notes, a feature that has been available in Microsoft Outlook for a long time. Note taking comes in handy in several situations but mostly for adding information to received or send email messages. This can be information that have been copied and pasted from somewhere else, contact information, tasks and basically anything else that is relevant but not part of the original email message.
The Thunderbird add-on tbNotes adds note taking capabilities to the email software. It’s current version is limited to Thunderbird 3 editions which are currently only available as beta versions (the official download version is still Thunderbird 2.x at the time of writing).
The add-on adds the capabilities to add, edit and remove notes in Thunderbird. The functionality becomes available after right-clicking an email message in Thunderbird. This opens the context menu with options to write, edit or remove notes.

It would be very confusing if there would not be an indicator if a note is available for an email. Users of the note taking add-on can add a new column to the email table layout in Thunderbird that indicates if notes are available.

This column is not available by default and needs to be added to the layout by clicking on the rightmost icon in the header display. It is furthermore possible to display all notes on a separate page in the email client. Filters are available on the page to reduce the amount of notes that are shown there. The page can be accessed at Tools > Notes.

The developer has lots of plans to extend the functionality of the add-on. Planned are a sidebar with notes categories or a special folder containing all the notes, adding notes to Thunderbird search and Lighting support so that notes can get automatically synced with the calendar add-on.
The tbNotes add-on can be downloaded from the Mozilla Thunderbird website. Keep in mind that it only works with Thunderbird 3.x clients.
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- CintaNotes Note Taking Software [Windows]
- Google Chrome Note Taking Extension Chromepad
- Email Client: Thunderbird 2.0.0.21
- Add a Calendar to Thunderbird
- Change The Thunderbird Reply Email Layout

I have been using the excellent Evernote 2 clipper with all versions of Thunderbird (currently 2.0.0.23) for notetaking. I use the local application of Evernote 2 and not the web version of Evernote.
Thunderbird has an add-on called XNote which I have been using for years.
https://addons.mozilla.org/en-US/thunderbird/addon/3093
Xnote and Evernote are two different types of applications for Thunderbird
Xnote is a sticky note taker whilst Evernote will copy part or a whole email by using the right click context menu. A local database of all notes taken is created.
The local application of Evernote used to work on earlier versions of Firefox but Firefox 3+ will now only work with the web-based Evernote application. A shame.
Just an info: when is the release of TB3?
Not sure. They plan to release a release candidate soon so it cannot be that far away anymore.