Yeah I do this as well. But since I sometimes have to share remote accounts, customizing the environment often devolves into dotfile edit wars over stuff like "set -o emacs".

Why not have your environment defined when you run something like the following in Bash:

    . clarkm.env 

That way you can each effectively have your own .bashrc. You could also have the following in your clarkm.env:

    unlink .emacs
    ln -s .emacs.clarkm .emacs

Or, if emacs supports it, alias in whatever command line flag that emacs uses to read from a different config file. Eg

    alias emacs="emacs --config .emacs.clarkm

I don't use emacs personally so the above will be inaccurate, but that kind of thing might work for you.