What happened to to the startup application preferences?
Solution 1:
The behavior I've discovered is the same as KDEs (local .desktops override system ones) so to be able to deselect/select items in 'Startup Applications' do this:
mkdir -p ~/.config/autostart # If not already created
cd ~/.config/autostart
cp /etc/xdg/autostart/*.desktop .
sed -i "s/NoDisplay=true/NoDisplay=false/g" *.desktop
Then pick your Startup Applications from the Startup Applications control panel. From there, "Log Out/Login" to apply (thanks to duffydack).
Solution 2:
This may help you: http://maketecheasier.com/disable-login-sound-in-ubuntu-oneiric-quick-tips/2011/09/15
Apparently, .desktop files now have an option to not appear in the startup application preferences in 11.10. Setting this option to FALSE, makes this items appear in the startup preferences and then you can disable it.
EDIT: As Jo-Erlend Schinstad said, the link may not be available. So, I'll explain the idea here.
The solution is to change the .desktop file of the application you want to see in the startup preferences. For example, for the login sound, you have to open the file:
gksudo gedit /usr/share/gnome/autostart/libcanberra-login-sound.desktop
Then change the line that says
NoDisplay=true
to
NoDisplay=false
Solution 3:
To enable them all again, run
find /etc/xdg/autostart/ -name "*.desktop" -exec sudo sed -i "s/NoDisplay=true/NoDisplay=false/g" '{}' \;
This will work but would only be temporary. For example:
dpkg -S /etc/xdg/autostart/ubuntuone-launch.desktop
ubuntuone-client: /etc/xdg/autostart/ubuntuone-launch.desktop
So if ubuntuone-client gets updated it will disappear from 'Startup Applications'. A developer told me when I had a similar situation with KDE to first copy the .desktop file to ~/.kde4/share/kde4/services/ and edit it there (the local one will override the system one); be nice if Gnome had this too here.