Gnome Shell Thunderbird Mail Notification
Just switched from unity to Gnome Shell, and I came across this very problem.
there is this script made by @tanwald that you can get on github. all that is left to do is to install th "install.sh"
(if you're not sure how to do it, follow these instrunctions here)
Thunderbird is integrated with the messaging indicator, so you will get notified of new email as long as Thunderbird is running.