SimpleDB (and recent DynamoDB) aren't suited to store files. Why don't you just make the versioning control on one of them, indexing files stored on S3?
You don't need to override the files on S3, as you can name them whatever you want and get the original name (and other info) from the database. You can even, for text files, for example, have a preview or the begining of the file on the DB or, for images, have a thumbnail on S3 and also get this info from the DB, so when users list the files they get only the thumbnail and, if they want, they download the full-size file.
Take a look at http://aws.amazon.com/en/dynamodb/faqs/#When_should_I_use_Amazon_DynamoDB_vs_Amazon_S3 and http://aws.amazon.com/en/running_databases/