I use subversion's in-place import (read for details) for configuration file version control in /etc and my home directory. It works well for me, but I've been seeing alot better/faster version control systems cropping up and want to convert. I tried mercurial, and it doesn't really support this feature of checking out a working copy of a single subfolder in a repository- it seems to want you to check out the whole thing at once.
Do other version control systems allow this? I've only tried cvs, mercurial, and subversion. Examples welcome.