accessibility/mousetweaks -> accessibility/mousetweaks3
audio/libcanberra -> audio/libcanberra-gtk3?
databases/evolution-data-server -> databases/evolution-data-server3
deskutils/gnome-utils -> deskutils/gnome-utils3
devel/libgdata -> devel/libgdata08 ? (api changes, may be patchable)
editors/gedit -> editors/gedit3
graphics/evince -> graphics/evince3
graphics/goocanvas -> graphics/goocanvas2
graphics/goocanvasmm -> graphics/goocanvasmm2
mail/evolution -> mail/evolution3
mail/evolution-exchange -> mail/evolution-exchange3
mail/evolution-mapi -> mail/evolution-mapi3
math/gcalctool -> math/gcalctool3
net/libgweather -> net/libgweather3
security/gnome-keyring -> security/gnome-keyring3
sysutils/brasero -> sysutils/brasero3
www/epiphany -> www/epiphany3
www/gtkhtml3 -> www/gtkhtml4
www/webkit-gtk2 -> www/webkit-gtk3
x11-fm/nautilus -> x11-fm/nautilus3
x11-themes/gnome-themes -> x11-themes/gnome-themes3
x11-themes/gtk-engines2 -> x11-themes/gtk-engines3
x11-toolkits/gtk20 -> x11-toolkits/gtk30
x11-toolkits/gtkmm24 -> x11-toolkits/gtkmm30
x11-toolkits/gtksourceview2 -> x11-toolkits/gtksourceview3
x11-toolkits/libwnck -> x11-toolkits/libwnck3
x11-toolkits/unique -> x11-toolkits/libunique3
x11-toolkits/vte -> x11-toolkits/vte3
x11/gnome-desktop -> gnome-desktop3
x11/gnome-panel -> x11/gnome-panel3
x11/gnome-screensaver -> x11/gnome-screensaver3
x11/gnome-terminal -> x11/gnome-terminal3
x11/gnome2 -> x11/gnome3
x11/libgnomekbd -> x11/libgnomekbd3
x11/yelp -> x11/yelp3
x11/zenity -> x11/zenity3