It took me a while to find a free software to backup files to Amazon S3 on Windows but here it is: Duplicati.
Duplicati is not only available for Windows but also for OS X and Linux (requires Mono though, better use Déjà Dup instead) and supports backups to Amazon S3, Google Drive and Microsoft SkyDrive. It offers AES-256 encryption, scheduling, multiple languages, file filters, bandwith options and much more.
Don’t get fooled by the Cloudberry advertisment, they don’t mention a price on their promo website, but they actually just offer a ‘free download’ of a trial version. Another commercial software with a free trial period would be Maluke S3 backup. But if you are willing to spend money, why not just donate to Duplicati.