These are the packages that I would merge, in order:

Calculating world dependencies  ..... ... ...done!
[blocks B     ] <=x11-themes/gnome-themes-2.8.2 (is blocking x11-themes/gtk-engines-2.6.3)
[blocks B     ] <app-admin/gnome-system-tools-1.1.91 (is blocking app-admin/system-tools-backends-1.2.0)
[ebuild     U ] sys-devel/gcc-config-1.3.11-r1 [1.3.10-r2] 
[ebuild     U ] dev-libs/atk-1.9.1 [1.8.0-r1] 
[ebuild     U ] x11-misc/shared-mime-info-0.16 [0.14-r2] 
[ebuild     U ] x11-libs/gtk+-2.6.7 [2.6.4-r1] 
[ebuild     U ] gnome-base/libglade-2.5.0 [2.4.2] 
[ebuild     U ] gnome-base/gconf-2.10.0 [2.8.1-r1] 
[ebuild     U ] gnome-base/libgnomecanvas-2.10.0 [2.8.0] 
[ebuild  NS   ] app-text/docbook-xml-simple-dtd-1.0  
[ebuild     U ] app-text/docbook-sgml-utils-0.6.14 [0.6.12] 
[ebuild     U ] gnome-base/gnome-vfs-2.10.0-r2 [2.8.4-r1] 
[ebuild     U ] gnome-base/libgnome-2.10.0 [2.8.1] 
[ebuild     U ] gnome-base/gnome-keyring-0.4.2 [0.4.1] 
[ebuild     U ] gnome-base/libgnomeui-2.10.0 [2.8.1-r1] 
[ebuild     U ] x11-themes/gnome-icon-theme-2.10.0 [2.8.0] 
[ebuild     U ] x11-themes/gtk-engines-2.6.3 [2.2.0] 
[ebuild     U ] x11-themes/gnome-themes-2.10.0 [2.8.2] 
[ebuild     U ] gnome-base/gnome-desktop-2.10.0 [2.8.3] 
[ebuild     U ] net-www/apache-2.0.54-r7 [2.0.54-r4] 
[ebuild     U ] gnome-base/librsvg-2.9.5 [2.8.1-r1] 
[ebuild  N    ] gnome-base/gnome-menus-2.10.0  
[ebuild     U ] gnome-base/eel-2.10.0 [2.8.2] 
[ebuild     U ] net-print/libgnomecups-0.2.0 [0.1.14] 
[ebuild     U ] gnome-base/libgnomeprint-2.10.0 [2.8.2] 
[ebuild     U ] gnome-base/libgnomeprintui-2.10.0.1 [2.8.2] 
[ebuild     U ] x11-libs/gtksourceview-1.2.0 [1.1.1] 
[ebuild     U ] app-editors/gedit-2.10.0 [2.8.3] 
[ebuild     U ] x11-libs/libxklavier-2.0 [1.04-r1] 
[ebuild     U ] media-libs/gst-plugins-0.8.8-r2 [0.8.8] 
[ebuild     U ] gnome-base/nautilus-2.10.0 [2.8.2-r1] 
[ebuild     U ] x11-wm/metacity-2.10.0 [2.8.13] 
[ebuild     U ] gnome-base/control-center-2.10.0 [2.8.2] 
[ebuild     U ] x11-libs/libwnck-2.10.0 [2.8.1-r1] 
[ebuild     U ] gnome-extra/evolution-data-server-1.2.1 [1.0.4] 
[ebuild     U ] gnome-base/gnome-panel-2.10.0 [2.8.3] 
[ebuild     U ] gnome-base/libgtop-2.10.0 [2.8.3] 
[ebuild  N    ] app-admin/system-tools-backends-1.2.0  
[ebuild     U ] gnome-base/gnome-applets-2.10.0 [2.8.2] 
[ebuild     U ] gnome-base/gnome-session-2.10.0 [2.8.1] 
[ebuild  NS   ] gnome-extra/gal-2.4.1  
[ebuild  NS   ] gnome-extra/libgtkhtml-3.6.1  
[ebuild     U ] mail-client/evolution-2.2.1.1 [2.0.4] 
[ebuild     U ] gnome-base/gdm-2.6.0.9-r2 [2.6.0.7] 
[ebuild     U ] gnome-extra/gnome-system-monitor-2.10.0 [2.8.3] 
[ebuild     U ] gnome-extra/zenity-2.10.0 [2.8.2] 
[ebuild     U ] gnome-extra/gconf-editor-2.10.0 [2.8.2] 
[ebuild     U ] app-arch/file-roller-2.10.0-r1 [2.8.4] 
[ebuild     U ] net-misc/vino-2.10.0 [2.8.1] 
[ebuild     U ] gnome-extra/nautilus-cd-burner-2.10.0 [2.8.7] 
[ebuild  N    ] media-plugins/gst-plugins-cdparanoia-0.8.8  
[ebuild     U ] gnome-extra/gnome-media-2.10.0 [2.8.0] 
[ebuild     U ] gnome-extra/gcalctool-5.5.41 [4.4.22] 
[ebuild     U ] dev-util/guile-1.6.7 [1.6.4-r1] 
[ebuild     U ] gnome-extra/gnome-games-2.10.0 [2.8.3] 
[ebuild     U ] gnome-extra/evolution-webcal-2.2.0 [2.0.1] 
[ebuild  N    ] app-text/gnome-doc-utils-0.1.3  
[ebuild     U ] gnome-extra/bug-buddy-2.10.0 [2.8.0] 
[ebuild     U ] gnome-extra/gnome-utils-2.10.0 [2.8.1] 
[ebuild     U ] app-text/gpdf-2.10.0 [2.8.3] 
[ebuild     U ] net-analyzer/gnome-netstatus-2.10.0 [2.8.0] 
[ebuild     U ] www-client/epiphany-1.6.0-r3 [1.4.8] 
[ebuild     U ] x11-libs/vte-0.11.12 [0.11.11-r2] 
[ebuild     U ] x11-terms/gnome-terminal-2.10.0 [2.8.2] 
[ebuild     U ] app-admin/gnome-system-tools-1.2.0-r1 [1.0.2-r1] 
[ebuild  NS   ] app-text/docbook-sgml-dtd-4.3-r1  
[ebuild     U ] app-admin/sudo-1.6.7_p5-r4 [1.6.7_p5-r2]