Chipaca & andrewsomething are both close... :)
The /desktop/gnome/session/required_components_list key lists the "components" that should be monitored by gnome-session, and restarted automatically when they exit. The default value for GNOME 2 is something like [windowmanager,panel,filemanager].
If you want to prevent nautilus (or whatever "filemanager component" you have configured) from getting (re)started by this mechanism, you can change the value to [windowmanager,panel]. (You can still have it start during login by adding it to the list of session start-up programs of course, but it won't get restarted automatically anymore.)
What application (with what commandline parameters) gets started for each component is defined under /desktop/gnome/session/required_components in a key with the name of the component. It is possible that more components are listed here than are used in the /desktop/gnome/session/required_components_list key.
Now, in case of nautilus, by default when it is not running yet it starts in the background, and if the /apps/nautilus/preferences/show_desktop key is set it also shows the Desktop. It is also possible to tell nautilus to behave differently with commandline parameters.
nautilus --sm-disable(user and sudo). This may have disabled the connection to the session-manager, but the session-manager kept right on restarting nautilus (with "nautilus --sm-disable" showing in the process list)... So does this parameter only take effect if it is applied at session startup (vs. mid-session), and are there any serious ramifications when disabled? (I think auto-mounting would vanish, but...? – Peter.O Dec 12 '10 at 01:08nautilus --sm-disablein an Undocumented Feature. So it's hard to say. But keep in mind that nautilus will restart as soon as it's killed, you'd have to start the first instance of it with this parameter.killall nautilus && nautilus --sm-disablewon't work. The command doesn't disable the feature for the running instances of nautilus. You might try to combine mine and andrewsomething's answer. ;-) – Stefano Palazzo Dec 12 '10 at 14:47killall -9 nautilus. – RolandiXor Dec 30 '10 at 12:09nautilus --sm-disabledoesn't work in Ubuntu 15.10 (Unknown option --sm-disable). Also there is no Gnome session. – Hubro Apr 01 '16 at 13:00