Came across the following suggestion for the best way of handling updates for your base Gentoo toolchain to maximize your system’s stability. For those that don’t know, your toolchain is the core system libraries and compiler (glibc, gcc, binutils, etc.). Even minor version bumps and patch updates can change the way your binaries are built so you owe it to yourself to re-emerge the system to keep things running smoothly, especially if you are using the unstable (‘~’ keyworded) branch of gcc/glibc.
emerge system && emerge system && emerge world and enjoy.
More info and a better explanation here