Based on this forum post by Alyssa, it looks like version support is coming soon at Amazon S3.

http://developer.amazonwebservices.com/connect/message.jspa?messageID=128502#128502

In the current release of Bucket Explorer, we save (automatically) a copy of the older version in a special bucket, every time a file is re-uploaded with the same name (& different content) again.  This functionality will be deprecated when Amazon starts supporting versioning natively in S3 API.

Until then, I believe we are the only one who support versioning, without changing file name or breaking the files in smaller propertiary chunks.