Can someone suggest some basic advice on dealing with web applications that interact with configuration files like httpd.conf, bind zone files, etc.

I understand that it's bad practice, in fact very dangerous to allow arbitrary execution of code without fully validating it and so on. But say you are tasked to write a small app that allows one to add vhosts to an apache configuration.

Do you have your code execute with full privileges, do you write future variables into a database and have a cron job (with full privileges) execute a script that pulls the vars from the database and throws them into a template config file, etc.

Some thoughts & contributions on this issue would be appreciated.

tl;dr - how can you securely write a web app to update/create entries in a config file like apache's httpd.conf, etc.