I've init-ed a git repo in my home directory... I'm not sure whether this was a good idea, but it seemed cool at the time. Most of the stuff in my dot files was just taken from various unremembered places I found through extensive Google searches and is probably not all that impressive.
If you look in .gitignore, you'll see /* which (in case you're not familiar) causes git to ignores all files. I then add files with git add -f path/to/file which makes git ignore the .gitignore for that file. Nifty.
Another neat thing about this is I can pretty easily deploy my dotfiles without having to run any scripts. I just clone the repo and move the .git directory to ~/ before checking out the latest version.
NOTE: You may want to back up the files by adding a branch and committing your old files to that (If you run git status, you'll see all the files which will be replaced by my files).