Find files that were not installed by the package manager

What you are looking for might be qfile. It is part of app-portage/portage-utils package and provides option -o or --orphans. You can use something like

find /usr/bin | xargs -I{} qfile -o {}

to get a list of orphaned files in /usr/bin.

Remark: Sadly, qfile in the current stable version of portage-utils, does not support readin from stdin, and the solution mentioned in the man page of qfile qfile -o $(find /usr/bin) does not work if the find result set is large, therefore we have to work around it a little bit, using xargs.

BTW, this is not something I myself came up with, but I found it at gossamer-threads, a comment by yvasilev.