In any event, the most recent problem I've seen is this (now old) block because com_err and ss were merged into the e2fsprogs/e2fsprogs-libs package on Gentoo. Emerge can't handle the block and leaves the user to 'take care of it manually'. Based on what I asked jeeves, this has caused many Gentoo users to break their systems. Here's the process that worked for me (based on http://www.odi.ch/weblog/posting.php?posting=524):
# emerge --fetchonly world
# quickpkg e2fsprogs com_err ss
# emerge -C ss com_err
# emerge -BO linux-headers
# emerge -K linux-headers
# emerge -BO util-linux
# emerge -K util-linux
# emerge -BO e2fsprogs e2fsprogs-libs
# emerge -K e2fsprogs e2fsprogs-libs
In order to upgrade anything else after that, I also had to re-emerge gcc (maybe I didn't, but it worked when I did):
# emerge -v gcc
# gcc-config <profileid>
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