Fantastic list with much more depth than I expected. Some surprises that others might be interested in from this article and comments below:
[1] Keeping buckets locked down and allowing direct client -> S3 uploads
[2] Using ALIAS records for easier redirection to core AWS resources instead of CNAMES.
[3] What's an ALIAS?
[-] Using IAM Roles
[4] Benefits of using a VPC
[-] Use '-' instead of '.' in S3 bucket names that will be accessed via HTTPS.
[-] Automatic security auditing (damn, entire section was eye-opening)
[-] Disable SSH in security groups to force you to get automation right.
Also, S3 buckets cannot scale infinitely. This is a huge myth http://aws.typepad.com/aws/2012/03/amazon-s3-performance-tip...