Comment 57 for bug 334344

Then fun fact is that even when 3.2 is release, it won't support notifications with NotifyOSD but will show its' own box a-la "Downloads complete" in Firefox. This is due to the inability of NotifyOSD to respond to actions (see comment: https://bugs.launchpad.net/ubuntu/+source/notify-osd/+bug/501393/comments/85). You can try current Thunderbird (3.2a1pre at the time of writing) with NotifyOSD and with vanilla notification-daemon.

I think it's a bit inappropriate, but I would like to point out this very nice addon for Thunderbird: https://addons.mozilla.org/thunderbird/addon/191033/

It "highlights" the Thunderbird window in window list when new message arrives, thus making it much easier to switch to it. It is certainly not a full replacement for proper libnotify/libindicate support.