The thing I like most about the project is that it allows me to use FTP services from anywhere with a full-featured client, requiring nothing more than a JRE. I'm terribly distraught that MS doesn't include a usable JRE by default, but hopefully this will change in the future.
My only suggestion for improving jFTP would be to make the software more like SSH Secure Shell, e.g. allow SSH login to machines and require only outbound connections on port 22. This would allow a user to conduct file transfer without an explicit FTP service running on the server, and would allow a user to download/upload files so long as the user has the right permissions on the server (e.g. no firewall holes or port forwarding required.) That said, I suppose such an addition would be appropriate for another software project (e.g. jSSH) rather than for extension as part of jFTP.
In any case, keep up the good work!
Perhaps the single coolest thing I've seen since the x8086 - too bad java web start isn't installed by default on more machines =(