Since I've started playing WoW again and doing a bit of multiboxing I figured out that keeping my WoW WTF folder in a Git repo is very handy. The WTF folder holds things like keybinds, window layouts, UI data, and addon data.
With this setup I can use scripts and other tools to automatically make changes to my WTF files without fear of messing anything up in an irreparable way. Plus I can easily see changes to files and such. All it takes is a "git init" and then "git commit" after I run WoW or make any manual/scripted changes.