After upgrading to WP 3.0 and the W3 Total Cache 0.9 dev release, it seems that mime types are not being set correctly when uploading to S3. Specifically, css/js is all being set to text/plain instead of the correct mime types, making browsers ignore them.
Everything was working fine before upgrading, so this is either something with WP 3 or the 0.9 dev release.
Any suggestions? Is this a known issue? Having to set everything manually is a bit annoying.