where is "startup applications" user config file for disabled and enabled applications?

Solution 1:

If you edit the files inside ~/.config/autostart/ they are written in this way:

[Desktop Entry]
Name=Dropbox
GenericName=File Synchronizer
Comment=Sync your files across computers and to the web
Exec=dropbox start -i
Hidden=false
Terminal=false
Type=Application
Icon=dropbox
Categories=Network;FileTransfer;
StartupNotify=false
X-GNOME-Autostart-enabled=false

The last line is the one that specifies if the app is enabled or not (check it by yourself with the gnome-session-properties enabling and disabling an app and noticing the change of that option in the file).

Then, you only have to copy all the files inside the folder to make a backup of that configuration.

Solution 2:

It does not store the data in a single file. The autostart files are copied into ~/.config/autostart when you configure them, and they are modified in there. So you should simply back up that directory if you wish to save that configuration.