I'm not that familiar with the inner workings of DNS, preferring to just add my CNAMEs and A records as appropriate, and leave the behind the scenes to other services. I host a few sites on Amazon S3, which clearly doesn't allow you to have an A record with a specific IP as it is a cloud service. Consequently, I have to use 301 redirects for the naked (foobar.org) domain to www.foobar.org, enforcing the use of either a third party service, or a server to do the redirects.
I noticed that Cloudflare have started offering a service which allows you essentially to break DNS conventions and set a CNAME for your root domain - solving the naked domain on S3 issue. However, I'm not sure what the issues are with this - is this going to cause issues for MX records, web visitors and others? What could be the unintended side effects?