Yeah, I go back and forth on that one. The problem is that the key management is crucial. Slip up and lose your key and your data is toast. Obviously this also applies to Amazon, but they have more resources, better incentives, and one million times the operational experience with their key management system than I'll ever have with mine. Frankly, my clients should bet on them over me.
Now, one good idea might be to redundantly back-up Amazon's backups at some other host, using GPG to encrypt those. This ensures against Amazon encryption errors, billing errors, mistyped legal injunctions, Jeff Bezos declaring you his personal enemy, et cetera.
This may be obvious, but rolling my own at-rest encryption is not going to significantly protect my data from an attacker who works inside Amazon, nor from an attacker who roots my instance. If the keys are in the cloud, the keys are in the cloud.
UPDATE: oh, yeah, I forgot the use case where you are writing to s3 from outside Amazon's datacenter over HTTPS. Okay, that is a much stronger case for GPG in advance. It wouldn't matter if we assumed that TLS always worked. But this is TLS. Does your upload client check the certificate chain? So many of them do not. I sure hope Amazon's CLI client does.....
