The Ubuntu Messaging Menu gives you quick access to email, chat and other social applications from your menu bar. If you want to hide some of the apps, though, you can remove them with a quick Terminal command.
If you prefer, say, Gmail to Evolution in Ubuntu, that "Set Up Email" entry in the messaging menu just gets in the way. To get rid of it (or any other entry in the menu), you can create a blacklist in the indicator's preferences. First, just create the blacklist directory by running the following command in the Terminal:
mkdir -p ~/.config/indicators/messages/applications-blacklist/
To add applications to the blacklist, just put symlinks to the applications in this folder. The indicators you can block are all available in /usr/share/indicators/messages/applications. So, to block Evolution, you just need to type:
ln -s /usr/share/indicators/messages/applications/evolution ~/.config/indicators/messages/applications-blacklist/evolution
You can rerun this command, replacing evolution with other apps you want to hide. Then, just restart the Gnome panel with killall gnome-panel to see the changes.
Alternatively, if you'd rather not see the Messaging Menu at all, you can uninstall it entirely by running:
sudo apt-get remove indicator-messages
Remove Unused Entries from the Ubuntu Messaging Menu [OMG! Ubuntu!]