vcsh allows you to have several git repositories, all maintaining their working trees in $HOME without clobbering each other.
That, in turn, means you can have one repository per config set (zsh, vim, ssh, etc), picking and choosing which configs you want to use on which machine.
It's been written for use with zsh, but it works with bash and even sh. Expect full support for /bin/sh soonish.
vcsh was designed with mr [1] in mind so you might want to install that, as well.
