One "simple way", or maybe more accurately, "portable/modular way" is to just add this to the bottom of your httpd.conf:
# Include site configurations
And then just copy a site's configuration from other examples you might have, and then put the site configuration in that directory, and then reload Apache. You may have to work out some errors here and there, and it is up to you to figure out the directory structure you want to use, and any custom logging. Here is a breakdown of what I used:
It was just thrown together, there may be a better way, and good reason to format it differently. In the site's configuration file I used the "/etc/httpd/conf.d/ssl.conf" as an example to create the SSL section. If you need any more examples, let me know and I can post up some more generic configuration examples from this setup.
If you want to ditch control panels and do it all from the console (which is what I do, and which is easier to automate) then I'd recommend using a distro like Debian on your VPS.
It already splits up your vhost sites like the example above. You can use 'a2ensite' and 'a2dissite' to enable and disable vhosts once you have a config file in /etc/apache2/sites-available and it'll symlink to /etc/apache2/sites-enabled. It does the same thing for Apache modules (a2enmod/a2dismod).
Jeff Standen, Chief of R&D, WebGroup Media LLC. - LinkedIn Cerb is a fast and flexible web-based platform for business collaboration and automation. http://www.cerbweb.com/
I actually got many of my examples from the Debian 5 distribution I had running on an old RaQ2. Debian is great for that, it takes a bit of a learning curve to work with the different way they handle the applications (say when compared to red-hat like distos), but it is very powerful.