This is a long, sad story... you have been warned.
Last week I was doing some pretty hardcore maintenance on my Gentoo servers and desktop. The main reason I started the work was due to the unmasking of GCC 4.1. My entire network is pretty automated thanks to Portage and a few dozen Python scripts, but compiler upgrades are something I don't usually automate (no good reason, just paranoid). In any case, I was poking around in the development environment and realized that one of the development servers was pretty crapped up, there where old packages everywhere. I went through the process of upgrading GCC on this development server and converted it over to USE="-*" (Gentoo users know what I mean), after all that I did a complete system audit and removed all the unused package and dependencies.
All of the cleanup and upgrades went incredibly well until I got the brilliant idea to go clean up /etc. Like a wise system administrator I tarred up the entire /etc directory just on the off-chance that I managed to screw it up, then I went to deleting things, lots of things. Somewhere in this process my ssh connection got killed completely silently and I was back on my laptop diligently deleting all things X and anything that didn't make sense on a server which was a lot! By the time I realized that I was no longer on the server it was WAY too late. Pretty much all my X, sound and desktop utility config files where gone. Naturally, I didn't have a backup of my laptop /etc because I had no intention of deleting anything on the laptop so I'm really screwed.
The end result was that I re-emerged the entire system and restored most of the config files to their defaults and hacked away at creating new ones. My plan now is to check the /etc directory on each of my systems into a Subversion repository and keep it updated every time I make any changes to my configuration. This should give me the benefit of not only having my /etc directory always available but also give me a complete history of the changes made in there too. Anybody else try anything like this before?