Having a unix-like system usually means lots of dotfiles cluttering up your home directory, providing user level configuration options for important packages. I'd prefer a dotless system, but in lieu of that here's my current configuration setup:
These are files used to maintain the collection, including a Makefile for building compiled versions of some files, and an all important sync script to copy the files to my home directory:
The W3T have a mantra: if it's not on the web it doesn't exist. I keep all of my dotfiles online not just so that they exist, but also so that a) I have distributed backups of them and revision control, and b) other people can learn from them just as I've done the same from many others. Since the files here are the masters, they're always up to date.
These are configuration files that I'm not currently using, but have used before, or that are dumps of state of current configurations:
This index page is automatically generated by a Python CGI (source), which itself is dependent on the sync script. This directory used to be powered by a rather wacky and intricate .htaccess—made with help from Rich Bowen, alias DrBacchus—but that system proved sadly too difficult to maintain.
Sean B. Palmer, inamidst.com