I thought I'd share my configuration of my Harmony 650 remote. I didn't think it's worthy of it's own thread, so I hope I'm not hijacking this thread here. [Edit by Chris!: I think it's worth it's own thread so I used my mod powers for good - not evil :) )
The media center (which I setup for my Father) is running Windows 7 using WMC for live & recorded TV and XBMC for downloaded movies & TV shows. I initially thought this may be tricky due to XBMC and WMC having overlaps in the default keymap for some of their functions. Play/pause/skip/etc are actioned by different keyboard commands. It is possible to edit XBMC's keymap, but upon inspecting it, I see it also recognises the WMC keyboard commands.
My Logitech Software profile is as follows:
Activity - Watch TV
TV - Sony
Receiver - Yamaha
Media center - Sony DVD recorder RDR-HX725 (This sends majority of the commands)
Media center - Apple TV (I've added this to fill in extra buttons that the Sony recorder couldn't fill and also to assign signals to custom buttons)
After setting up the activity to implement all four devices, I went into the customise buttons screen. I filled in any gaps of buttons which weren't assigned and also made custom buttons for the LCD screen on the remote. These custom LCD buttons were what I used the Apple TV for, I just assigned random actions.
To setup Flirc, I opened the keyboard map and went through the WMC keyboard map from their website, assigning all the buttons that were relevant. There were one or two buttons left over which I could use in XBMC. I also assigned the custom buttons (such as launching certain programs, close (alt+f4), and other windows functions.
So far, this is working flawlessly. There might be a quicker way of doing things, but this way I know exactly what is assigned to what.
I don't know where I found out about Flirc, but I've got to say that I'm extremely happy I stumbled upon it. You guys have an amazing product here :)