$ ln -sf .dotfiles/{.bash,.bash_profile,.bashrc,.gitconfig,.hgrc,.inputrc,.pythonrc.py,.screenrc,.terminfo,.vim,.vimrc} .
$ ln -s .dotfiles/.ssh/config .ssh/
+Symlink the git hooks
+ $ cd .dotfiles && rm -rf hooks && ln -s ../git-hooks hooks
You can add machine specific configs to the bash init scripts by creating files in ~/.bash called environment_local, interactive_local, functions_local, etc
Also, learn how to use Git and use it to version control other config files of yours.