In Ubuntu 11.4 the traditional notification area has been replaced by a new API called libappindicator. Some applications, such as Shutter, are written in Perl and so cannot easily implement support for libappindicator (which currently just has bindings for C, Python, and Mono).
There is a way to workaround this though as Unity maintains a default white-list of applications that are permitted in the notification area.
To see the current notification white-list open the Terminal and type the following:
gsettings get com.canonical.Unity.Panel systray-whitelist
You should this this command return something like this:
['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray']
Select the results and copy it into a text editor – add your application to the list and append it to the gsettings set command as per the example below.
gsettings set com.canonical.Unity.Panel systray-whitelist "['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray', 'Shutter']"
Then log off and on and you should see your application in the notification area when you open it.
Obviously you can use this technique to remove applications from the notification area too. Just don’t go crazy adding every application under the sun or you’ll suffer notification overload (which this was designed to mitigate).