Ganymed SSH-2, the robust SSH implementation used in Cyberduck, is now maintained at Google Code and includes the optimizations patches that I have made for Cyberduck. Most prominently that is parallelism for downloads and uploads increasing transfer rates.
We recently did an in-depth session to analyze the reasons of inferior SFTP throughput rates for file transfers compared to OpenSSH. We have a resolution that should give much better results now that makes use of parallel requests in the SFTP protocol layer.
You can switch to the latest beta build that includes the fix to give it a try. If you are in the private beta for Windows, use Check for Update… to update automatically.