normal portage (2.0.49_pre16):

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

Calculating world dependencies  ...done!
[ebuild     U ] media-libs/netpbm-10.11.10 [10.11.5-r2] -svga 
[ebuild     U ] media-sound/esound-0.2.31 [0.2.29-r1] +tcpd +alsa 
[ebuild     U ] gnome-base/bonobo-activation-2.2.4 [2.2.3] -doc 
[ebuild     U ] dev-db/mysql-4.0.14-r1 [4.0.14] -static +readline +innodb +berkdb +tcpd +ssl +perl -debug 
[ebuild     U ] media-libs/gdk-pixbuf-0.22.0-r1 [0.22.0] -doc 
[ebuild     U ] net-libs/nss_ldap-210 [209.1] +berkdb -debug +ssl 
[ebuild     U ] sys-apps/attr-2.4.7 [2.4.1] -nls -debug 
[ebuild     U ] sys-apps/acl-2.2.13 [2.1.1-r1] 
[ebuild     U ] sys-kernel/ac-sources-2.4.22_rc2-r1 [2.4.22_pre10-r1] -build -doc +tcltk 
[ebuild     U ] media-libs/libvorbis-1.0-r4 [1.0-r3] +sse -3dnow 
[ebuild     U ] app-admin/mirrorselect-0.81 [0.8] 
[ebuild     U ] app-admin/ufed-0.34 [0.33] 
[ebuild     U ] sys-kernel/mm-sources-2.6.0_beta3-r2 [2.6.0_beta3-r1] -doc +tcltk 
[ebuild     U ] gnome-base/libgtop-2.0.3 [2.0.2-r1] 
[ebuild     U ] gnome-base/gdm-2.4.1.6 [2.4.1.4] 
[ebuild  N    ] media-libs/speex-1.0.1  +oggvorbis +sse 
[ebuild     U ] media-libs/xine-lib-1_rc0-r2 [1_beta12-r1] +arts +esd +avi -nls +dvd +aalib +X +directfb +oggvorbis +alsa +gnome 
[ebuild     U ] media-video/xine-ui-0.9.22 [0.9.21] +X +aalib +gnome -nls +directfb -lirc 
[ebuild     U ] sys-libs/libcap-1.10-r1 [1.10] +python 


Patched portage:

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

Calculating world dependencies  ...done!
[ebuild     U ] media-libs/netpbm-10.11.10 [10.11.5-r2] S[0] -svga 
[ebuild     U ] media-sound/esound-0.2.31 [0.2.29-r1] S[0] +tcpd +alsa 
[ebuild     U ] gnome-base/bonobo-activation-2.2.4 [2.2.3] S[0] -doc 
[ebuild     U ] dev-db/mysql-4.0.14-r1 [4.0.14] S[0] -static +readline +innodb +berkdb +tcpd +ssl +perl -debug 
[ebuild     U ] media-libs/gdk-pixbuf-0.22.0-r1 [0.22.0] S[0] -doc 
[ebuild     U ] net-libs/nss_ldap-210 [209.1] S[0] +berkdb -debug +ssl 
[ebuild     U ] sys-apps/attr-2.4.7 [2.4.1] S[0] -nls -debug 
[ebuild     U ] sys-apps/acl-2.2.13 [2.1.1-r1] S[0] 
[ebuild     U-] sys-kernel/ac-sources-2.4.22_rc2-r1  S[2.4.22-rc2-ac1] -build -doc +tcltk 
[ebuild     U ] media-libs/libvorbis-1.0-r4 [1.0-r3] S[0] +sse -3dnow 
[ebuild     U ] app-admin/mirrorselect-0.81 [0.8] S[0] 
[ebuild     U ] app-admin/ufed-0.34 [0.33] S[0] 
[blocks B     ] gnome-base/gnome-session (from pkg gnome-base/gnome-core-1.4.2-r1)
[blocks B     ] gnome-base/gnome-desktop (from pkg gnome-base/gnome-core-1.4.2-r1)
[blocks B     ] x11-terms/gnome-terminal (from pkg gnome-base/gnome-core-1.4.2-r1)
[ebuild  N    ] gnome-base/gnome-core-1.4.2-r1  S[0] -kde -nls +cups 
[ebuild  N    ] dev-util/guile-1.6.4  S[12] 
[ebuild     U-] gnome-base/libgtop-1.0.13-r2  S[1] -nls 
[ebuild     U-] gnome-base/gnome-applets-1.4.0.5  S[1] -nls 
[ebuild  N    ] dev-libs/librep-0.16.2  S[0] +readline 
[ebuild  N    ] x11-libs/rep-gtk-0.15-r3  S[1.2] +gnome 
[ebuild  N    ] x11-wm/sawfish-1.0.1-r6  S[0] +gtk -nls +esd +gnome 
[ebuild  N    ] gnome-extra/medusa-0.5.1-r3  S[0] -nls 
[ebuild     U-] gnome-base/librsvg-1.0.3  S[1] 
[ebuild     U-] gnome-base/eel-1.0.2-r3  S[1] -nls 
[ebuild     UD] gnome-base/nautilus-1.0.6-r9 [2.2.4] S[0] -nls +mozilla 
[ebuild     UD] gnome-base/gdm-2.2.5.4-r5 [2.4.1.4] S[0] -nls +gnome 
[ebuild     U-] gnome-base/gnome-1.4-r3  S[1.4] 
[ebuild     U ] gnome-base/libgtop-2.0.3 [2.0.2-r1] S[2] 
[ebuild     U ] gnome-base/gdm-2.4.1.6 [2.4.1.4] S[0] 
[ebuild  N    ] media-libs/speex-1.0.1  S[0] +oggvorbis +sse 
[ebuild     U ] media-libs/xine-lib-1_rc0-r2 [1_beta12-r1] S[0] +arts +esd +avi -nls +dvd +aalib +X +directfb +oggvorbis +alsa +gnome 
[ebuild     U ] media-video/xine-ui-0.9.22 [0.9.21] S[0] +X +aalib +gnome -nls +directfb -lirc 
[ebuild     U ] sys-libs/libcap-1.10-r1 [1.10] S[0] +python