The amd64 handbook http://www.gentoo.org/doc/en/handbook/handbook-amd64.xml?full=1 mentiones /etc/portage/make.conf (resp. /mnt/gentoo/etc/portage/make.conf). However, in the current stage3 tarball stage3-amd64-20120621.tar.bz2 the file make.conf in located in etc/make.conf
I just read "eselect news read", which explains everything 2012-09-09-make.conf-and-make.profile-move Title make.conf and make.profile move Author Jorge Manuel B. S. Vicetto <jmbsvicetto@gentoo.org> Posted 2012-09-09 Revision 1 Starting next week, new stages will have make.conf and make.profile moved from /etc to /etc/portage. This is a change in the installation defaults, that will only affect new installs so it doesn't affect current systems. Current users don't need to do anything. But if you want to follow the preferred location, you may want to take the chance to move the files in your system(s) to the new location.