I use a single Harmony remote for my LG TV, Denon AVR, Windows PC and JRiver. Everything is fully integrated and the PC even goes to sleep when I power off and wakes up when I power on. The magic that ties it all together is a Flirc
http://flirc.tv/.
The Flirc is a little USB programmable keyboard with an IR receiver. You use a simple utility to program it to press any keyboard key/combination using any remote button. Combine this with the free utility Autohotkey and you then can invoke any command like starting JRiver, putting the computer to sleep, rebooting etc... Over the years I tried several remotes and IR receivers but nothing ever worked perfectly until I found the Flirc.
A trick I learned with the Harmony was to program it for your TV and AVR model as required and then just include any other TV that you don't have to control the PC and JRiver. It doesn't matter what TV model you select you just want a bunch of free available IR signals that won't affect your TV and AVR. You then use this phantom TV to program the Flirc. This saves you a device on the Harmony because if you use a Media Center device to send PC key codes you will need at least two devices and may bump you up to a higher model Harmony.
Just one thing, the Flirc is easy to program but you will need some Windows technical knowledge to integrate it all with Autohotkey. It's really nothing very hard though.
Check out the Flirc, it really is an awesome device. I have two I use for JRver and XBMC.