After a recent update in Ubuntu 14.04 Trusty Tahr, it's possible to whitelist or blacklist individual applications from using the Ubuntu AppMenu (global menu).
These settings are accessible via Dconf-editor, under com > canonical > unity-gtk-module.
To blacklist an application from using the Unity global menu in Ubuntu 14.04, install dconf-editor:
sudo apt-get install dconf-editor
Then open Dconf Editor, navigate to com > canonical > unity-gtk-module and add the binary name of the application(s) you want under "blacklist" or "whitelist". After adding some application(s) to the blacklist or whitelist, restart that application(s) or log out and log back in.
Example 1: to blacklist Gedit, add the following under com > canonical > unity-gtk-module > blacklist:
Example 2: to blacklist Gedit, Nemo and Audacious, add the following under com > canonical > unity-gtk-module > blacklist:
['gedit', 'nemo', 'audacious']
In the same way you can force applications to use the global menu by adding them under "whitelist". Applications that are blacklisted by default include: Eclipse, Acroread, Emacs and Freeciv.