Found a way of adding Skype to messaging menu by reading other posts around the web such as this one on omgubuntu, might help you do the same with gm-notify but I can't say for sure that it will. Here's what I did after looking for instructions for adding skype to the messaging menu:
Open a terminal and first check that the app you want is there by going to /usr/share/applications and then running ls. Use filters as there will be a lot of results depending on how many applications you have installed.
ls s* will return results for skype and skype-wrapper, use ls g* instead to return results for gm-notify.
You should see something like skype.desktop, skype-wrapper.desktop and possibly (though not for sure since it isn't installed on my system) gm-notify.desktop
- If there's there, brilliant, we can get a bit further with the solution. Now you want to open a text editor and make a file for the application you're trying to add. I'm more comfortable with nano as it avoid opening yet another window and having terminal running, so I'd run:
sudo nano /usr/share/indicators/messages/applications/skype
assuming that you are adding a reference for skype or skype-wrapper. Replace /skype with /gm-notify if that's what you want to add. Or, if you're uncomfortable with command line and want a normal text editor like gedit, run:
gksu gedit /usr/share/indicators/messages/applications/skype
Enter your password when prompted, it won't appear on screen but you need to enter it correctly and press the enter key. You'll now have a new text file open in your text editor named for your application. All it does is tell the Messaging Menu where your application's .desktop file is, which is why we checked that one existed earlier. As an example, here's my /usr/share/indicators/messages/applications/skype file:
Notice that I've invoked skype-wrapper.desktop and not skype.desktop. It's purely because I made the file for skype.desktop originally and didn't bother renaming it. Save and close. For those running nano, you press Control+O to save, then press enter to confirm, then press Control+X to exit.
Now you need to logout and log back in for the changes to take effect. You should find a new item in your messaging menu named 'skype' assuming that you followed my instructions. It'll launch Skype when you click it. Should also work for gm-notify