We're big fans of RightScale. Their developer version is free and pretty much that's all we use at the initial stages. We use S3, EC2, EBS, Cloudfront, SQS, etc. They have tools for tweaking all of those built-in so it makes life easier. Of course we have our own tools, too, (mostly with boto) but their GUI does come in handy. We manage pretty much all of our EC2 instances through that, with easy image bundling, java SSH consoles, etc.

There are a few other good services/tools out there, but so far I haven't found any as full-featured as RightScale. (But I'm watching this thread for other suggestions, too.)

I wish their upper-tier stuff was less expensive and we'd experiment with it a bit more. Supposedly it's free for companies who are funded through YC, though.