I'm a web designer who uses Cyberduck regularly on both an iMac and MacBook Pro for ftp. I have just two suggestions for you to implement in a future update.
Firstly, to send you this ticket I had to create an account, verify my email and sign in. Is this really necessary? Could you not just have an email link in the help section of the menubar?
Secondly, if you are running Cyberduck in several different spaces on a Mac, when you upload or download a file, the transfer window will open in the window you started Cyberduck in, despite the fact you are now in a different one. Because of this, you can't tell a transfer has started because you can't see the transfer window so you drop the file into the window again and start multiple files uploading. It is a small point but it would be really useful if there was a transfer bar for each individual window. It could be part of the browsing window itself and just slide into view at the top when a transfer starts and the slide away after it's finished. Just an idea....
On my computer, when uploading a file into a Cyberduck window in a Space other than the one with the Transfer window, the Space will suddenly shift to the one with the Transfer window, annoyingly. This must be because I have Preferences->Transfers->General->"Bring widow to front when transfer starts" checked. I agree with the bug submitter: the Transfers window needs to be overhauled, and should be linked to its upload window.