Actually, that is one area where the Harmony topped any and every universal I've ever used. Somehow, my Sony DVD/Receiver thingie (no comments from the gallery) uses a remote that nobody else knows how to put into their universal. But the harmony does it on the computer, so you type in the make and model and it has a database online of thousands of systems that it just downloads the information for. It found my DVD/Receiver thingie and does a great job of controlling it.
You download the controls for new devices and customize the settings while it's hooked up via USB to your PC. The list of available operations is sometimes not exact. Maybe a button on your remote is called Replay and it's listing says "SkipBack" or something, but it's generally close enough that you can figure it out.
Doing it on your PC is actually great, but the downside for me is my computer is upstairs and my TV is downstairs, so I have to fiddle with the settings, upload them to the remote, then run downstairs to test them to make sure they work, then run back upstairs and remember the tweaks I want to make. A bit of a hassle but still plenty worth it.