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Currently when you receive a message in GNOME Shell, the notification is displayed for a few seconds and that's about it - you can't tell if you have new messages unless you take a look at the message tray, which is hidden by default.

So if you often miss IM notifications in GNOME Shell, you can use an extension called Shell Message Notifier which displays the number of conversations with unread messages on the top GNOME Shell bar (in my test it only worked with Empathy).

Update: it seems the extension works with any application that displays a notification counter in the message tray (so for instance, it works with Mailnag too).

The extension is very simple and doesn't do anything else so nothing will happen if you click the notification icon on the top bar:

The extension is unpolished, it does very little, the code is horrible and I didn’t pay any attention to usability; I just wanted a quick fix while waiting for upstream to fix the bug properly. Nevertheless, I hope this code will be useful for other people too!

- Marco Barisione, the extension developer

Ubuntu 11.10 users can use our GNOME 3 PPA to install Shell Message Notifier:
sudo add-apt-repository ppa:webupd8team/gnome3
sudo apt-get update
sudo apt-get install gnome-shell-message-notifier

Once installed, reload GNOME Shell (press ALT + F2 and enter "r" or log out and log back in), enable the extension and then restart GNOME Shell once again.

For other Linux distributions, install it using the commands below:
git clone git://git.collabora.co.uk/git/user/bari/shell-message-notifier.git
cd shell-message-notifier
make install

Then follow the instructions (it's not a typical "make install").