gconf has (stupidly) made simple things much complicated — the very same file will lookes completely different by diff:

$ wdiff /root/.gconf/desktop/gnome/applications/window_manager/%gconf.xml ~crewbase/.gconf/desktop/gnome/applications/window_manager/%gconf.xml
<?xml version="1.0"?>
<gconf><entry name="default" [-mtime="1047921198" muser="root"-] {+mtime="1047933896" muser="crewbase"+} type="string"><stringvalue>/usr/bin/sawfish</stringvalue></entry></gconf>

Conf files that really holds my tweaking.

$ xsel -p | xargs ls -gG --time-style=+''
-rw-------    1        0  .gconf/apps/gnome-settings/%gconf.xml
-rw-------    1      192  .gconf/apps/gnome-settings/gnome-panel/%gconf.xml
-rw-------    1        0  .gconf/apps/gnome-terminal/%gconf.xml
-rw-------    1        0  .gconf/apps/gnome-terminal/profiles/%gconf.xml
-rw-------    1     1001  .gconf/apps/gnome-terminal/profiles/Default/%gconf.xml

$ cat .gconf/apps/gnome-settings/gnome-panel/%gconf.xml
<?xml version="1.0"?>
<gconf><entry name="history-gnome-run" mtime="1047918832" muser="root" type="list" ltype="string"><li type="string"><stringvalue>xterm</stringvalue></li></entry></gconf>

put .gconf/apps/gnome-terminal/profiles/Default/%gconf.xml in vcs.

Files get setup when gnome launched.

$ find .gconf | sort
.gconf
.gconf/%gconf.xml
.gconf/apps
.gconf/apps/%gconf.xml
.gconf/apps/panel
.gconf/apps/panel/%gconf.xml
.gconf/apps/panel/profiles
.gconf/apps/panel/profiles/%gconf.xml
.gconf/apps/panel/profiles/default
.gconf/apps/panel/profiles/default/%gconf.xml
.gconf/apps/panel/profiles/default/applets
.gconf/apps/panel/profiles/default/applets/%gconf.xml
.gconf/apps/panel/profiles/default/applets/clock_applet
.gconf/apps/panel/profiles/default/applets/clock_applet/%gconf.xml
.gconf/apps/panel/profiles/default/applets/clock_applet/prefs
.gconf/apps/panel/profiles/default/applets/clock_applet/prefs/%gconf.xml
.gconf/apps/panel/profiles/default/applets/mixer_applet
.gconf/apps/panel/profiles/default/applets/mixer_applet/%gconf.xml
.gconf/apps/panel/profiles/default/applets/pager_applet
.gconf/apps/panel/profiles/default/applets/pager_applet/%gconf.xml
.gconf/apps/panel/profiles/default/applets/pager_applet/prefs
.gconf/apps/panel/profiles/default/applets/pager_applet/prefs/%gconf.xml
.gconf/apps/panel/profiles/default/applets/tasklist_applet
.gconf/apps/panel/profiles/default/applets/tasklist_applet/%gconf.xml
.gconf/apps/panel/profiles/default/applets/tasklist_applet/prefs
.gconf/apps/panel/profiles/default/applets/tasklist_applet/prefs/%gconf.xml
.gconf/apps/panel/profiles/default/applets/tray_applet
.gconf/apps/panel/profiles/default/applets/tray_applet/%gconf.xml
.gconf/apps/panel/profiles/default/general
.gconf/apps/panel/profiles/default/general/%gconf.xml
.gconf/apps/panel/profiles/default/objects
.gconf/apps/panel/profiles/default/objects/%gconf.xml
.gconf/apps/panel/profiles/default/objects/email_launcher
.gconf/apps/panel/profiles/default/objects/email_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/help_launcher
.gconf/apps/panel/profiles/default/objects/help_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/main_menu
.gconf/apps/panel/profiles/default/objects/main_menu/%gconf.xml
.gconf/apps/panel/profiles/default/objects/presentations_launcher
.gconf/apps/panel/profiles/default/objects/presentations_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/spreadsheet_launcher
.gconf/apps/panel/profiles/default/objects/spreadsheet_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/terminal_launcher
.gconf/apps/panel/profiles/default/objects/terminal_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/web_browser_launcher
.gconf/apps/panel/profiles/default/objects/web_browser_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/objects/wordprocessor_launcher
.gconf/apps/panel/profiles/default/objects/wordprocessor_launcher/%gconf.xml
.gconf/apps/panel/profiles/default/panels
.gconf/apps/panel/profiles/default/panels/%gconf.xml
.gconf/apps/panel/profiles/default/panels/bottom_panel
.gconf/apps/panel/profiles/default/panels/bottom_panel/%gconf.xml
.gconf/desktop
.gconf/desktop/%gconf.xml
.gconf/desktop/gnome
.gconf/desktop/gnome/%gconf.xml
.gconf/desktop/gnome/accessibility
.gconf/desktop/gnome/accessibility/%gconf.xml
.gconf/desktop/gnome/accessibility/keyboard
.gconf/desktop/gnome/accessibility/keyboard/%gconf.xml
.gconf/desktop/gnome/applications
.gconf/desktop/gnome/applications/%gconf.xml
.gconf/desktop/gnome/applications/window_manager
.gconf/desktop/gnome/applications/window_manager/%gconf.xml