I can't find any description of the difference between the EBS and S3 images.
Is there some documentation somewhere that I've missed?
The content is the same. The difference lies in the device that backs the root partition.
In general, EBS is newer and should be preferred because it's easier to customise (if you want to customise it in the future).
You can read all about the differences here, but I don't recommend it unless you really want to know how they work: http://serverfault.com/questions/113184/should-i-persist-images-on-ebs-or-s3
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