I take advantage of the fact that a .emacs file has higher precedence than a .emacs.d/init.el file for this. All the common stuff lives in the .emacs.d directory and is under source control. The little bit of work/machine specific stuff I have goes in the .emacs file, which wraps a

    (load "~/.emacs.d/init")

My home machines don't need anything special, so there's no .emacs file and the .emacs.d/init.el file just gets loaded directly.