I think I've finally set my R50 the way I wanted, and the Harmony 550 can go to the dumpster. My setup (HTPC, receiver, plasma display) is quite straightforward as everything is controled through the HTPC except volume and power, but I think the process can be applied to more complex situations. I always wanted to control the entire system (no matter how complex) as one coherent unit using one remote with buttons in natural positions controlling the correct device -- I don't want to switch between devices and activities. The way I do this is copy and paste groups of buttons to the Main and Favorite screens (volume from the receiver and everything else from the HTPC), and defining the On and Off buttons to power all the devices.
Harmony 550 and URC-R50.
Actions on the main screen - these are actually devices (doesn't matter which ones - they're never used), but macros do the required action. The last step in each macro is always the MAIN button press, so the screen doesn't change. The selection of images is very limited, though. Also I find it very limiting that the labels are limited to 7 letters per line, even though 10 or more can easily fit.
Actual devices - they are on the third page as they're not intended for normal use, and I may hide them later. Note that there are multiple devices for Microsoft Media Center HTPC and the Sony Receiver as the presets are not complete on a single device. I was also very pleased that the presets had discrete ON/OFF codes for the Panasonic 7UY plasma display, which I wasn't able to find anywhere, and thought didn't exist at all.
Media Center factory presets -- pretty unusable:
Favorite Channels - kinda gimmicky, as the keystrokes are transmitted slowly, but it does work. What's interesting is that it can store a lot more macros (as long as they are single device, which in my setup is quite possible)