When I was setting up the bitcoin.exe with -server argument, and had to create/edit the config file, it was a little confusing.  I was getting help on IRC, but the syntax of the config file entries were given to me wrong, so I wound up wasting a lot of time over something very simple.

What about having a config file and having all settings displayed in there.  Lines could either be commented-out or features could be set to OFF or values just be blank.  I remember when some programs would use .ini files for these sort of things, with different headings for different categories of settings.  It was actually kind of convenient.