Yes, I am doing exactly what you're talking about, and using only one Apple Remote to do it. If you hold the Menu and Play buttons on the Apple Remote for several seconds, the remote will change its ID number, making it appear to be a new remote. In Remote Buddy's preferences, under Hardware, if enable multiple Apple Remotes, any time you press a button on your Apple Remote, Remote Buddy will register the remote under its distinct ID.

I've programmed my Logitech Harmony 550 with the Apple Remote using several different Apple Remote ID numbers, naming each device in the Harmony software something indicative of which Harmony buttons I want the Apple Remote ID to correspond to (playback 1, playback 2, channels, navigation, macros 1, macros 2, etc.). Each time I have the Harmony learn a new Apple Remote ID, I also point the Apple Remote at the Mac to have Remote Buddy learn the ID at the same time. Then I create and name virtual Apple Remotes within Remote Buddy to match the ones on the Harmony remote and match the virtuals to their proper IDs. Finally, at present, I'm working up several Harmony activity configurations, each of which maps several Apple Remotes to different sets of keys on the Harmony, and several Remote Buddy mappings to have the respective virtual Apple Remotes perform their proper actions in each application.

It is an astoundingly arduous process, but it's relatively straightforward, and it will allow me to use a very robust remote to control my Mac mini, TV, and audio receiver, without a silly-looking IR receiver hanging off the mini.

Felix, I would absolutely love to package up this configuration, once I have it polished, so that others don't have to go through this laborious process. Of course, I would also need to be able to replicate and distribute my Harmony configuration, which might not be possible, but can I at least bundle up the virtual Apple Remotes and their respective mappings in Remote Buddy to distribute to other users?