In going over the Q&A transcript, I noticed the following questions that I did not get to:

How do I backup a Drupal website that gets both the database and the filesystem in an clean snapshot that can fully restore the site after a crash?

and

what is the best way to maintain a test or development environment that can be used to test changes before they are pushed out to the production site?

I wanted to give some additional resources for answering these questions.  Ultimately, your solutions to these will vary depending on your specific needs, but in general for backing up your site I would recommend keeping your code in your version control system of choice (svn, git, whatever you like) and then check out the backup and migrate module for simplifying database backups.

The answer to the second question is somewhat more complicated, but I would start by looking at the features module.  This allows you to export some of your configuration that is stored in the database into code that you can then deploy on your production site.  It's a very cool way to address the problem of reconciling your code with your database.

I also highly recommend checking out the September 2010 issue of Linux Journal.  It has a great article by Jerad Bitner and Nate Haug that goes into some best practices for managing larger Drupal sites.  Yes, a shameless plug, but it really is useful. :)

I would like to point you at some really good information on Lullabot.com: http://www.lullabot.com/podcasts/drupal-voices-114-kathleen-murtagh-on-…

This post links to a few sources of information on deployment methods, and I highly recommend checking it out.