I have done it this way, but I do not think it is a very good solution. You can go to /usr/share/applications and delete the applications .desktop files that you do no want to show up in the GNOME 'All Applications'. However, I recommned not to delete but move the applications you do not want to use to another separate folder. Because, if ever you want the application you removed to show up again in 'All Applications' you can just move it back again to /usr/share/applications.