Reflux ftw?

Most addons have profiles. I know that profiles can get messy but what I do to fix that is have the main profile set to Default(A lot will create one for each character) and then delete every other profile. Makes everything a lot less cluttered.

I use git to save my addon settings. It was created for version control of source code, and lua saved variables are... plain text source code :) Wouldn't matter if they weren't of course, but it's still a nice coincidence. Just create a repository to track the WTF folder and remember to commit after any changes to your ui and voila! A history of your addon settings that you can step through at will. Made some changes that you don't like and want to undo? Want to step back to the way you had it set up 2 months ago (my addon config changes frequently...)? Git lets you do this.

Unfortunately, no wow addon for it yet.

Never heard of these, but I'll look em up anyway.

Tevildo: I tried to use a vcs but gave up because wow (or ace or whatever) randomly rearranges the tables in the settings so it's very hard to track what has actually changed.

I do kinda the same thing as Mgssidley. I create a profile for the add-on called "Default" and I set it to how I will want it to look and work. Then on every character, I create a profile for them (with the same name), copy the default profile, and then tweak it how I want it for that toon. 99% of my UI is the same across the board for all my characters, but I also get slight customization that I need (I needed grid for my healer to be slightly different for example).

I had a crash that destroyed my grid settings only twice and yeah it's annoying to rebuild that but it was only grid. My other addons that change the layout are hard coded to do their job. They don't have profiles that can be messed up. The minimap will always stay at the same place as will the oUF layout, the chat boxes, the quest tracker and all those tiny modifications that I have.