emerge -pDuvN world

These are the packages that would be merged, in order:

Calculating world dependencies -
!!! Ebuilds for the following packages are either all
!!! masked or don't exist:
media-sound/xmms media-plugins/xmms-mpg123 app-text/gpdf

... done!
[ebuild  N    ] virtual/glut-1.0  0 kB
[ebuild  N    ] dev-util/indent-2.2.9-r2  USE="nls" 662 kB
[ebuild  NS   ] gnome-base/orbit-0.5.17-r1  1,040 kB
[ebuild  NS   ] sys-libs/db-1.85-r2  279 kB
[ebuild  N    ] gnome-base/gnome-libs-1.4.2  USE="esd nls -doc -kde" 2,807 kB
[ebuild  N    ] dev-libs/libxml-1.8.17-r2  USE="-doc" 972 kB
[ebuild  N    ] gnome-base/oaf-0.6.10  USE="nls" 425 kB
[ebuild  NS   ] gnome-base/gconf-1.0.9  USE="nls" 765 kB
[ebuild  NS   ] gnome-base/gnome-common-1.2.4-r4  152 kB
[ebuild  NS   ] gnome-base/gnome-vfs-1.0.5-r4  USE="nls ssl -doc" 1,024 kB
[ebuild  N    ] media-libs/gdk-pixbuf-0.22.0-r5  USE="X mmx -doc" 388 kB
[ebuild  NS   ] gnome-base/librsvg-1.0.3  208 kB
[ebuild  NS   ] gnome-base/libglade-0.17-r6  USE="X nls -bonobo" 409 kB
[ebuild  NS   ] gnome-base/control-center-1.4.0.5-r2  USE="nls -debug" 3,303 kB
[ebuild  NS   ] gnome-base/gnome-panel-1.4.2-r2  USE="nls -kde" 6,129 kB
[ebuild  N    ] gnome-base/gnome-print-0.37  USE="nls" 750 kB
[ebuild  N    ] gnome-base/bonobo-1.0.22  USE="nls" 1,158 kB
[ebuild  N    ] gnome-base/libghttp-1.0.9-r4  143 kB
[ebuild  NS   ] gnome-base/eel-1.0.2-r3  USE="nls" 941 kB
[ebuild     UD] gnome-base/nautilus-1.0.6-r10 [2.14.1] USE="nls%* (-X%*) (-beagle%) (-debug%) (-gnome%*)" 11,212 kB
[ebuild  N    ] dev-perl/Compress-Raw-Zlib-2.001  201 kB
[ebuild  N    ] virtual/perl-Scalar-List-Utils-1.18  0 kB
[ebuild  N    ] dev-perl/IO-Compress-Base-2.001  87 kB
[ebuild  N    ] dev-perl/IO-Compress-Zlib-2.001  128 kB
[ebuild     U ] dev-perl/Compress-Zlib-2.001 [1.41] 60 kB
[ebuild  NS   ] app-text/docbook-xml-dtd-4.2-r1  76 kB
[ebuild     U ] gnome-base/gnome-volume-manager-1.5.15-r3 [1.5.15-r2] USE="crypt -debug -doc" 0 kB
[ebuild     U ] media-libs/imlib2-1.3.0 [1.2.1.009] USE="X bzip2 gif jpeg mmx mp3 nls png zlib -doc -tiff" 933 kB

Total size of downloads: 34,264 kB

emerge -pv --depclean

*** WARNING ***  Depclean may break link level dependencies.  Thus, it is
*** WARNING ***  recommended to use a tool such as `revdep-rebuild` (from
*** WARNING ***  app-portage/gentoolkit) in order to detect such breakage.
*** WARNING ***
*** WARNING ***  Also study the list of packages to be cleaned for any obvious
*** WARNING ***  mistakes. Packages that are part of the world set will always
*** WARNING ***  be kept.  They can be manually added to this set with
*** WARNING ***  `emerge --noreplace <atom>`.
*** WARNING ***
*** WARNING ***  As a safety measure, depclean will not remove any packages
*** WARNING ***  unless *all* required dependencies have been resolved.  As a
*** WARNING ***  consequence, it is often necessary to run
*** WARNING ***  `emerge --update --deep world` prior to depclean.

Calculating dependencies... done!

Dependencies could not be completely resolved due to
the following required packages not being installed:

=app-text/docbook-xml-dtd-4.2-r1 required by gnome-extra/bug-buddy-2.14.0
=x11-libs/qt-3.3.4-r8 required by kde-base/kdelibs-3.4.3-r1
=sys-devel/autoconf-2.5* required by media-plugins/xmms-mpg123-1.2.10-r1 media-plugins/xmms-alsa-1.2.10-r2 media-plugins/xmms-esd-1.2.10-r1 media-plugins/xmms-oss-1.2.10 media-plugins/xmms-vorbis-1.2.10-r1 media-plugins/xmms-mikmod-1.2.10
virtual/glut required by dev-python/pyopengl-2.0.0.44 x11-apps/mesa-progs-6.5.1 media-libs/gle-3.0.1-r2 media-libs/jasper-1.701.0
<gnome-base/nautilus-2 required by x11-themes/nautilus-themes-1.0

Have you forgotten to run `emerge --update --deep world` prior to depclean?