In Gnome (Ubuntu's default Desktop Environment). the Startup Applications are .desktop files stored in
~/.config/autostart
Also, as already mentioned, both Gnome and Xfce also stores system-wide "default" startup applications in
/etc/xdg/autostart
And the enable/disable feature is provided by the attribute
X-GNOME-Autostart-enabled=true (or false)
in each .desktop file
If a user toggles enable/disable status of a given application (without deleting it) that was in the system folder, it is copied to the user folder and then the attribute X-GNOME-Autostart-enabled is changed. If a user deletes a given application from the list, the .desktop is copied to user folder with the Hidden=true attribute (or the file is simply deleted if it was present just in the user folder)
Last but not least, files in both user and system folder are not marked as executable. Permission is 644 (rw-r--r--)