The next major release of Cyberduck will support Amazon S3. I have integrated the excellent open source library JetS3t into Cyberduck. It allows you to transfer files to your S3 account and browse the S3 buckets and files in a hierarchical way as you are used to with other remote file systems supported by Cyberduck.
Cyberduck 3.0 is expected to be released later this month. The current nightly build (use with caution) is available for testing.