If there is anything that I dislike on gnome-shell are the notifications...wait, not the notifications itself, I really like the whole bottom hot corner concept and stuff. But it's very easy for me, specially at my work that I use dual monitors, to miss an im message that way.
I then started to search for a shell extension that provides something to alert me of the existence of an unread notification. I found the Pidgin Persistent Notification's concept very good and decided to try to do a generic one (since it's pidgin specific). This is the result:
It supports any shell version >= 3.2. You can download it on extensions.gnome at the link: Gnome-Shell Notifications Alert
The source code is on github <https://github.com/hackedbellini/Gnome-Shell-Notifications-Alert> and licensed at GPLv2. Fell free to fork it! Just don't forget to send me a pull request, so I can merge your improvements into the official code ;D