While looking for a solution to my VMWare / USB issue, I came across a Linux.com article:
Developer crafts Linux support for Logitech Harmony remote controls.
Instead of using the Windows GUI to program the remote, you use the Logitech website (the windows gui is basically a fancy version of that). When you are done, you download a .EZHex file which you can then sync in Linux to your remote.
I haven’t tried it yet, though it is on my list of things to do. For those who have stayed away from the Logitech Harmony remotes because they required Windows, you need no longer live in the dark ages of remote controls.