You can turn on or off or add applications you want to run each time you log in to Ubuntu/Gnome (specifically Ubuntu v10.10, Gnome v2.32.0) by clicking System->Preferences->Startup Applications, but if you want to actually add/remove/turn on/off items via a script, you’ll need to know that the startup items exist as .desktop files in the location ~/.config/autostart/*.desktop

To find out about the structure of a .desktop file, see http://library.gnome.org/admin/system-admin-guide/stable/menustructure-desktopentry.html.en

Also in the general area is the ~/.config/menus directory where you can manipulate the entire menu structure.  See more about how this works at http://library.gnome.org/admin/system-admin-guide/stable/menustructure-13.html.en