A common good practice (as I see it) is to have a fully-fledged configuration file example in the documentation, e.g for a Linux based distribution foo a file /usr/share/doc/foo/example/foo.conf.example - that way the actual configuration file /etc/foo/foo.conf can be kept clean without clutter.

Don't know about Windows best practices though. A Windows Help File pair *.chm/*.chw comes to mind, which would contain all possible configuration items.