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

Calculating dependencies  
Parent:    None
Depstring: sys-apps/portage
Candidates: ['sys-apps/portage']
ebuild: sys-apps/portage-2.0.51_rc1
binpkg: None

Parent:    ebuild / sys-apps/portage-2.0.51_rc1 nomerge
Depstring:  !build? ( >=sys-apps/sed-4.0.5 dev-python/python-fchksum >=dev-lang/python-2.2.1 sys-apps/debianutils >=app-shells/bash-2.05a ) selinux? ( dev-python/python-selinux )
Candidates: ['>=sys-apps/sed-4.0.5', 'dev-python/python-fchksum', 'sys-apps/debianutils', '>=app-shells/bash-2.05a', '>=dev-lang/python-2.2.1']
ebuild: sys-apps/sed-4.0.9
binpkg: None

Parent:    ebuild / sys-apps/sed-4.0.9 nomerge
Depstring: virtual/libc nls? ( sys-devel/gettext ) sys-devel/gnuconfig virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/gnuconfig', 'sys-devel/gettext']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None

Parent:    ebuild / sys-libs/glibc-2.3.4.20040808 nomerge
Depstring: >=sys-devel/gcc-3.2.3-r1 nptl? ( >=sys-devel/gcc-3.3.1-r1 ) >=sys-devel/binutils-2.14.90.0.6-r1 virtual/os-headers nptl? ( >=sys-kernel/linux26-headers-2.6.5 ) nls? ( sys-devel/gettext ) !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/patch ) sys-devel/gcc virtual/os-headers sys-apps/baselayout nls? ( sys-devel/gettext )
Candidates: ['>=sys-devel/gcc-3.2.3-r1', 'sys-devel/patch', 'sys-devel/gettext', 'sys-apps/baselayout', 'sys-kernel/linux-headers', '>=sys-devel/binutils-2.14.90.0.6-r1', 'sys-devel/gcc']
ebuild: sys-devel/gcc-3.4.1-r2
binpkg: None

Parent:    ebuild / sys-devel/gcc-3.4.1-r2 merge
Depstring: virtual/libc !uclibc? ( >=sys-libs/glibc-2.3.3_pre20040420-r1 ) !uclibc? ( hardened? ( >=sys-libs/glibc-2.3.3_pre20040529 ) ) ( !sys-devel/hardened-gcc ) >=sys-devel/binutils-2.14.90.0.8-r1 amd64? ( >=sys-devel/binutils-2.15.90.0.1.1-r1 ) >=sys-devel/bison-1.875 >=sys-devel/gcc-config-1.3.1 amd64? ( multilib? ( >=app-emulation/emul-linux-x86-baselibs-1.0 ) ) !build? ( gcj? ( gtk? ( >=x11-libs/gtk+-2.2 ) ) ) !build? ( gcj? ( >=media-libs/libart_lgpl-2.1 ) ) !build? ( >=sys-libs/ncurses-5.2-r2 nls? ( sys-devel/gettext ) ) !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/libtool ) sys-devel/gnuconfig virtual/libc !uclibc? ( >=sys-libs/glibc-2.3.3_pre20040420-r1 ) !uclibc? ( hardened? ( >=sys-libs/glibc-2.3.3_pre20040529 ) ) >=sys-devel/gcc-config-1.3.1 >=sys-libs/zlib-1.1.4 >=sys-apps/texinfo-4.2-r4 !build? ( >=sys-libs/ncurses-5.2-r2 )
Candidates: ['>=sys-devel/binutils-2.14.90.0.8-r1', '>=sys-libs/ncurses-5.2-r2', '>=sys-devel/gcc-4.2-r4', '>=sys-devel/bison-1.875', '>=sys-devel/gcc-config-1.3.1', 'sys-devel/patch', 'sys-devel/gettext', '!sys-devel/hardened-gcc', 'sys-devel/libtool', 'sys-libs/glibc', '>=sys-libs/zlib-1.1.4', '>=sys-libs/glibc-2.3.3_pre20040420-r1', 'sys-devel/gnuconfig']
ebuild: sys-devel/binutils-2.15.90.0.1.1-r3
binpkg: None

Parent:    ebuild / sys-devel/binutils-2.15.90.0.1.1-r3 nomerge
Depstring: virtual/libc nls? ( sys-devel/gettext ) !build? ( !bootstrap? ( dev-lang/perl ) ) !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/libtool ) sys-devel/gnuconfig virtual/libc nls? ( sys-devel/gettext ) !build? ( !bootstrap? ( dev-lang/perl ) )
Candidates: ['dev-lang/perl', 'sys-devel/patch', 'sys-devel/gettext', 'sys-devel/libtool', 'sys-libs/glibc', 'sys-devel/gnuconfig']
ebuild: dev-lang/perl-5.8.5
binpkg: None

Parent:    ebuild / dev-lang/perl-5.8.5 nomerge
Depstring: !uclibc? ( sys-apps/groff ) berkdb? ( sys-libs/db ) gdbm? ( >=sys-libs/gdbm-1.8.0 ) >=sys-apps/portage-2.0.48-r4 >=sys-devel/libperl-5.8.5 !<dev-perl/ExtUtils-MakeMaker-6.17 !<dev-perl/File-Spec-0.84-r1 !<dev-perl/Test-Simple-0.47-r1 !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/patch ) sys-devel/gcc berkdb? ( sys-libs/db ) gdbm? ( >=sys-libs/gdbm-1.8.0 )
Candidates: ['sys-libs/db', '!<dev-perl/ExtUtils-MakeMaker-6.17', '!<dev-perl/File-Spec-0.84-r1', 'sys-devel/patch', '!<dev-perl/Test-Simple-0.47-r1', '>=sys-devel/libperl-5.8.5', '>=sys-libs/gdbm-1.8.0', 'sys-apps/groff', '>=sys-apps/portage-2.0.48-r4']
ebuild: sys-libs/db-4.2.52_p2
binpkg: None

Parent:    ebuild / sys-libs/db-4.2.52_p2 nomerge
Depstring: tcltk? ( >=dev-lang/tcl-8.4 ) java? ( virtual/jdk ) !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig tcltk? ( dev-lang/tcl ) java? ( virtual/jre )
Candidates: ['sys-devel/gnuconfig', 'dev-java/blackdown-jre', 'sys-devel/patch', 'dev-java/blackdown-jdk']
ebuild: sys-devel/gnuconfig-20040214
binpkg: None

Parent:    ebuild / sys-devel/gnuconfig-20040214 nomerge
Depstring: !bootstrap? ( sys-devel/patch ) 
Candidates: ['sys-devel/patch']
ebuild: sys-devel/patch-2.5.9
binpkg: None

Parent:    ebuild / sys-devel/patch-2.5.9 nomerge
Depstring: virtual/libc virtual/libc
Candidates: ['sys-libs/glibc']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
Exiting... ebuild / sys-devel/patch-2.5.9 nomerge
Exiting... ebuild / sys-devel/gnuconfig-20040214 nomerge
ebuild: dev-java/blackdown-jre-1.4.1
binpkg: None

Parent:    ebuild / dev-java/blackdown-jre-1.4.1 merge
Depstring: virtual/libc amd64? ( >=app-emulation/emul-linux-x86-baselibs-1 ) >=dev-java/java-config-0.2.5 >=sys-apps/sed-4 !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/patch ) sys-devel/gcc virtual/libc amd64? ( >=app-emulation/emul-linux-x86-baselibs-1 ) >=dev-java/java-config-0.2.5 >=sys-apps/sed-4 sparc? ( >=sys-devel/gcc-3.2 ) amd64? ( >=sys-devel/gcc-3.2 )
Candidates: ['sys-libs/glibc', '>=sys-apps/sed-4', 'sys-devel/patch', '>=dev-java/java-config-0.2.5']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-apps/sed-4.0.9
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: dev-java/java-config-1.2.10
binpkg: None

Parent:    ebuild / dev-java/java-config-1.2.10 nomerge
Depstring: !bootstrap? ( sys-devel/patch ) virtual/python virtual/python
Candidates: ['dev-lang/python', 'sys-devel/patch']
ebuild: dev-lang/python-2.3.4
binpkg: None

Parent:    ebuild / dev-lang/python-2.3.4 nomerge
Depstring: virtual/libc >=sys-libs/zlib-1.1.3 !build? ( X? ( tcltk? ( >=dev-lang/tk-8.0 ) ) ncurses? ( >=sys-libs/ncurses-5.2 readline? ( >=sys-libs/readline-4.1 ) ) berkdb? ( >=sys-libs/db-3.1 ) gdbm? ( sys-libs/gdbm ) ssl? ( dev-libs/openssl ) doc? ( =dev-python/python-docs-2.3.4* ) dev-libs/expat ) !bootstrap? ( sys-devel/patch ) virtual/libc >=sys-libs/zlib-1.1.3 !build? ( X? ( tcltk? ( >=dev-lang/tk-8.0 ) ) ncurses? ( >=sys-libs/ncurses-5.2 readline? ( >=sys-libs/readline-4.1 ) ) berkdb? ( >=sys-libs/db-3.1 ) gdbm? ( sys-libs/gdbm ) ssl? ( dev-libs/openssl ) doc? ( =dev-python/python-docs-2.3.4* ) dev-libs/expat ) dev-python/python-fchksum
Candidates: ['dev-python/python-fchksum', '>=sys-libs/readline-4.1', 'dev-libs/openssl', 'sys-libs/gdbm', '>=sys-libs/db-3.1', 'dev-libs/expat', '>=sys-libs/ncurses-5.2', 'sys-devel/patch', 'sys-libs/glibc', '>=sys-libs/zlib-1.1.3']
ebuild: dev-python/python-fchksum-1.7.1
binpkg: None

Parent:    ebuild / dev-python/python-fchksum-1.7.1 nomerge
Depstring: sys-libs/zlib sys-libs/zlib
Candidates: ['sys-libs/zlib']
ebuild: sys-libs/zlib-1.2.1-r3
binpkg: None

Parent:    ebuild / sys-libs/zlib-1.2.1-r3 nomerge
Depstring: virtual/libc !bootstrap? ( sys-devel/patch ) virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-libs/zlib-1.2.1-r3 nomerge
Exiting... ebuild / dev-python/python-fchksum-1.7.1 nomerge
ebuild: sys-libs/readline-5.0
binpkg: None

Parent:    ebuild / sys-libs/readline-5.0 nomerge
Depstring: >=app-shells/bash-2.05b-r2 >=sys-libs/ncurses-5.2-r2 !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig >=app-shells/bash-2.05b-r2 >=sys-libs/ncurses-5.2-r2
Candidates: ['sys-devel/gnuconfig', '>=app-shells/bash-2.05b-r2', '>=sys-libs/ncurses-5.2-r2', 'sys-devel/patch']
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
ebuild: app-shells/bash-3.0-r5
binpkg: None

Parent:    ebuild / app-shells/bash-3.0-r5 nomerge
Depstring: >=sys-libs/ncurses-5.2-r2 !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig 
Candidates: ['sys-devel/gnuconfig', '>=sys-libs/ncurses-5.2-r2', 'sys-devel/patch']
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
ebuild: sys-libs/ncurses-5.4-r5
binpkg: None

Parent:    ebuild / sys-libs/ncurses-5.4-r5 nomerge
Depstring: virtual/libc !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/gnuconfig', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-libs/ncurses-5.4-r5 nomerge
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / app-shells/bash-3.0-r5 nomerge
ebuild: sys-libs/ncurses-5.4-r5
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-libs/readline-5.0 nomerge
ebuild: dev-libs/openssl-0.9.7d-r1
binpkg: None

Parent:    ebuild / dev-libs/openssl-0.9.7d-r1 nomerge
Depstring: virtual/libc sys-apps/diffutils >=dev-lang/perl-5 >=sys-apps/sed-4 !uclibc? ( sys-devel/bc ) !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/patch ) sys-devel/gcc virtual/libc
Candidates: ['sys-devel/bc', '>=sys-apps/sed-4', 'sys-apps/diffutils', 'sys-devel/patch', '>=dev-lang/perl-5', 'sys-libs/glibc']
ebuild: sys-devel/bc-1.06-r5
binpkg: None

Parent:    ebuild / sys-devel/bc-1.06-r5 nomerge
Depstring: readline? ( >=sys-libs/readline-4.1 >=sys-libs/ncurses-5.2 ) >=sys-apps/portage-2.0.47-r10 sys-devel/flex !bootstrap? ( sys-devel/patch ) readline? ( >=sys-libs/readline-4.1 >=sys-libs/ncurses-5.2 )
Candidates: ['>=sys-libs/ncurses-5.2', '>=sys-libs/readline-4.1', 'sys-devel/patch', 'sys-devel/flex', '>=sys-apps/portage-2.0.47-r10']
ebuild: sys-libs/ncurses-5.4-r5
binpkg: None
ebuild: sys-libs/readline-5.0
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: sys-devel/flex-2.5.4a-r5
binpkg: None

Parent:    ebuild / sys-devel/flex-2.5.4a-r5 nomerge
Depstring: virtual/libc !bootstrap? ( sys-devel/patch ) virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-devel/flex-2.5.4a-r5 nomerge
ebuild: sys-apps/portage-2.0.51_rc1
binpkg: None
Exiting... ebuild / sys-devel/bc-1.06-r5 nomerge
ebuild: sys-apps/sed-4.0.9
binpkg: None
ebuild: sys-apps/diffutils-2.8.7
binpkg: None

Parent:    ebuild / sys-apps/diffutils-2.8.7 nomerge
Depstring: virtual/libc >=sys-apps/portage-2.0.47-r10 >=sys-apps/sed-4 nls? ( sys-devel/gettext ) !build? ( sys-apps/texinfo sys-apps/help2man ) !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig virtual/libc
Candidates: ['>=sys-apps/portage-2.0.47-r10', '>=sys-apps/sed-4', 'sys-devel/patch', 'sys-devel/gettext', 'sys-apps/help2man', 'sys-libs/glibc', 'sys-devel/gnuconfig']
ebuild: sys-apps/portage-2.0.51_rc1
binpkg: None
ebuild: sys-apps/sed-4.0.9
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: sys-devel/gettext-0.12.1-r1
binpkg: None

Parent:    ebuild / sys-devel/gettext-0.12.1-r1 nomerge
Depstring: virtual/libc !bootstrap? ( sys-devel/patch ) sys-devel/gnuconfig virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/gnuconfig', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-devel/gettext-0.12.1-r1 nomerge
ebuild: sys-apps/help2man-1.33.1
binpkg: None

Parent:    ebuild / sys-apps/help2man-1.33.1 nomerge
Depstring: dev-lang/perl nls? ( dev-perl/Locale-gettext >=sys-devel/gettext-0.12.1-r1 ) dev-lang/perl nls? ( dev-perl/Locale-gettext >=sys-devel/gettext-0.12.1-r1 )
Candidates: ['dev-perl/Locale-gettext', '>=sys-devel/gettext-0.12.1-r1', 'dev-lang/perl']
ebuild: dev-perl/Locale-gettext-1.01-r1
binpkg: None

Parent:    ebuild / dev-perl/Locale-gettext-1.01-r1 nomerge
Depstring: sys-devel/gettext >=dev-lang/perl-5.8.2 !<dev-perl/ExtUtils-MakeMaker-6.17 sys-devel/gettext
Candidates: ['>=dev-lang/perl-5.8.2', '!<dev-perl/ExtUtils-MakeMaker-6.17', 'sys-devel/gettext']
ebuild: dev-lang/perl-5.8.5
binpkg: None
Myparent ebuild / dev-perl/Locale-gettext-1.01-r1 nomerge
ebuild: sys-devel/gettext-0.12.1-r1
binpkg: None
Exiting... ebuild / dev-perl/Locale-gettext-1.01-r1 nomerge
ebuild: sys-devel/gettext-0.12.1-r1
binpkg: None
ebuild: dev-lang/perl-5.8.5
binpkg: None
Exiting... ebuild / sys-apps/help2man-1.33.1 nomerge
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
Exiting... ebuild / sys-apps/diffutils-2.8.7 nomerge
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: dev-lang/perl-5.8.5
binpkg: None
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
Exiting... ebuild / dev-libs/openssl-0.9.7d-r1 nomerge
ebuild: sys-libs/gdbm-1.8.3-r1
binpkg: None

Parent:    ebuild / sys-libs/gdbm-1.8.3-r1 nomerge
Depstring: virtual/libc berkdb? ( =sys-libs/db-1* ) sys-devel/gnuconfig !bootstrap? ( sys-devel/patch ) virtual/libc
Candidates: ['sys-libs/glibc', '=sys-libs/db-1*', 'sys-devel/gnuconfig', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-libs/db-1.85-r2
binpkg: None

Parent:    ebuild / sys-libs/db-1.85-r2 nomerge
Depstring: virtual/libc !bootstrap? ( sys-devel/patch ) virtual/libc
Candidates: ['sys-libs/glibc', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-libs/db-1.85-r2 nomerge
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / sys-libs/gdbm-1.8.3-r1 nomerge
ebuild: sys-libs/db-4.2.52_p2
binpkg: None
ebuild: dev-libs/expat-1.95.7-r1
binpkg: None

Parent:    ebuild / dev-libs/expat-1.95.7-r1 nomerge
Depstring: virtual/libc makecheck? ( >=dev-libs/check-0.8 ) sys-devel/gnuconfig virtual/libc makecheck? ( >=dev-libs/check-0.8 )
Candidates: ['sys-libs/glibc', 'sys-devel/gnuconfig']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-devel/gnuconfig-20040214
binpkg: None
Exiting... ebuild / dev-libs/expat-1.95.7-r1 nomerge
ebuild: sys-libs/ncurses-5.4-r5
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: sys-libs/zlib-1.2.1-r3
binpkg: None
Exiting... ebuild / dev-lang/python-2.3.4 nomerge
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / dev-java/java-config-1.2.10 nomerge
Exiting... ebuild / dev-java/blackdown-jre-1.4.1 merge
ebuild: sys-devel/patch-2.5.9
binpkg: None
ebuild: dev-java/blackdown-jdk-1.4.2_rc1-r1
binpkg: None

Parent:    ebuild / dev-java/blackdown-jdk-1.4.2_rc1-r1 nomerge
Depstring: virtual/libc >=dev-java/java-config-0.2.6 doc? ( =dev-java/java-sdk-docs-1.4.2* ) !bootstrap? ( sys-devel/patch ) virtual/libc >=dev-java/java-config-0.2.6 doc? ( =dev-java/java-sdk-docs-1.4.2* )
Candidates: ['sys-libs/glibc', '>=dev-java/java-config-0.2.6', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None
ebuild: dev-java/java-config-1.2.10
binpkg: None
ebuild: sys-devel/patch-2.5.9
binpkg: None
Exiting... ebuild / dev-java/blackdown-jdk-1.4.2_rc1-r1 nomerge
Exiting... ebuild / sys-libs/db-4.2.52_p2 nomerge
Myparent ebuild / dev-lang/perl-5.8.5 nomerge
Myparent ebuild / dev-lang/perl-5.8.5 nomerge
ebuild: sys-devel/patch-2.5.9
binpkg: None
Myparent ebuild / dev-lang/perl-5.8.5 nomerge
ebuild: sys-devel/libperl-5.8.5
binpkg: None

Parent:    ebuild / sys-devel/libperl-5.8.5 nomerge
Depstring: !uclibc? ( sys-apps/groff ) berkdb? ( sys-libs/db ) gdbm? ( >=sys-libs/gdbm-1.8.0 ) >=sys-apps/portage-2.0.45-r4 !bootstrap? ( sys-devel/patch ) berkdb? ( sys-libs/db ) gdbm? ( >=sys-libs/gdbm-1.8.0 )
Candidates: ['sys-apps/groff', 'sys-libs/db', '>=sys-apps/portage-2.0.45-r4', 'sys-devel/patch', '>=sys-libs/gdbm-1.8.0']
ebuild: sys-apps/groff-1.19.1
binpkg: None

Parent:    ebuild / sys-apps/groff-1.19.1 merge
Depstring: virtual/libc >=sys-apps/texinfo-4.0 !bootstrap? ( sys-devel/patch ) !bootstrap? ( sys-devel/patch ) sys-devel/gcc virtual/libc >=sys-apps/texinfo-4.0
Candidates: ['sys-libs/glibc', '>=sys-devel/gcc-4.0', 'sys-devel/patch']
ebuild: sys-libs/glibc-2.3.4.20040808
binpkg: None

emerge: there are no ebuilds to satisfy ">=sys-devel/gcc-4.0".