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.
WebDAV on the upcoming Lion release of Mac OS X will feature a more prominent role. As a superset of HTTP, WebDAV adds support to retrieve a directory hierarchy and create, change and move documents therein. WebDAV is a core protocol supported in Cyberduck since 2008. To make it more robut and ready for the next couple of years I have decided to contribute to the Sardine project, an open source implementation of the WebDAV protocol that is now used in Cyberduck. You can test the new implementation in the latest beta build.