Things change rapidly in the WordPress world. The content in this post is more than a year old and may no longer represent best practices.
Greg Turner described the way he uses the Meta Box plugin to help him create custom metaboxes on client sites. His presentation slides took the form of a custom theme design. I can embed the presentation here, but it doesn’t scale, so it’s better to go visit the site: http://cmb.zenofwp.com.