A hacker I know (who has I team I believe - the debuggable.com guys - both successful bloggers and core teamembers of the cakephp community) has been working on transload.it for a while, it's a pretty good service despite still being in beta, but I haven't put it through its paces like I'm sure you would. (I was working on a wordpress plugin.) It sits on ec2 and will save right into your s3.
I don't know their plans for the full release, but they could be a way to break out of your lock in with encoding.com.