in 11.04 I can go to system->preferences ->startup applications and do things like uncheck Gnome Login Sound when I open Startup Applications in 11.10 the screen is empty
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:
Then change the line that says
To enable them all again, run
This will work but would only be temporary. For example:
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.
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:
Then pick your Startup Applications from the Startup Applications control panel. From there, "Log Out/Login" to apply (thanks to duffydack).