I see several people describing how to do this for a custom domain with sub-domain but no one talking about how to do it without one.
Example: Setting foobar.com and w
Since this question was asked things have changed. It is now possible to host your site on S3 with a root domain.
Instead of just having one bucket named "www.yourserver.com", you have to create another bucket with the nude (root) domain name, e.g. "yourserver.com".
After that you will have to use Amazon's DNS service Route 53. Create an A record for the nude domain and a CNAME for the "www" hostname.
Note that you will need to move the domain management of your domain to Amazon Route 53 completely.
See for the detailled walk-through here: http://docs.aws.amazon.com/AmazonS3/latest/dev/website-hosting-custom-domain-walkthrough.html