A dedicated backup plugin or service like Blogvault is the best way to back up a WordPress site. A service like this will back up your website and keep old copies so that you can restore the website to any previous snapshot up to one year ago. If you want to perform a manual backup, you'll have to create an archive with all of the existing files within the WordPress folder and export the database of the current website. Performing manual backups on large sites can become very complex and unreliable very quickly.