I am using Ubuntu 12.04 and I know the GUI way to maintain the startup program list but now I want to find out the way to add/remove startup applications using a command line interface (CLI).
In your home directory, there's a folder called .config/autostart. Anything placed in this folder will be run when you login. This could be accomplished through the command line by creating the .desktop file with the command
nano ~/.config/autostart/blah.desktop. If you like to find out about the syntax of .desktop files, you can visit Freedesktop and Gnome.