The main problem is that you are using the ->command field of
GnomeVFSMIMEApplication a lot. This is deprecated and will fail to work for
desktop entries with an Exec value like "myapp %u --enable-blah". If possible it
would be good to just use gnome_vfs_mime_application_launch, otherwise you
should use gnome_vfs_mime_application_get_exec and correctly expand the macros
(see gnome-vfs-mime-handlers.c expand_application_parameters).