This is a problem we're going to face many times.
I don't see commented out config as a solution. First, at this point, when the file is re-written following an update, comments are lost. That may change, but in general using the file as documentation is fragile. Second, if we added commented out sections for all the various options different subsystems may want to expose, we'll soon have a 1,00 line file full of confusing stuff.
I think we're going to need a mix of things to solve this:
1) Ship a few different canned configs files for the most common profiles, with the user able to select which they want via a command line switch.
2) An "examples" dir in the dist where some less common choices can be highlighted.
3) Most importantly, an installer application where users can easily tell us what subsystems they want in their profile. This is the most important part; #1 is mostly to provide a very easy out-of-the-box experience.