Update for Windows 7 Users
Hi all and thanks for all of this great information. This is my first post out here but since a lot of the information on this thread is "older" I thought I'd share my experience with Windows MCE remotes. First here is a rundown of my system and items I encountered:
I received the MCE remote and Harmony today and proceeded to setup the MCE remote first. I simply plugged the IR receiver into a free USB port and Windows 7 had no problems recognizing it and loading the proper drivers. After some fiddling around with the remote it seemed like once in Boxee the arrows and back functions worked properly. As far as I can tell there was nothing special needed to make Boxee work with a properly setup MCE remote although I found that several of the buttons will actually call up WMC.
The Harmony was/is my solution to solve all of that. Being able to customize buttons on the Harmony remote while eliminating some of the unused commands from the MCE remote makes life pretty simple. After several hours of tinkering I finally was able to get the Harmony remote setup properly. Effectively, when I hit the "watch movies" button the PC comes out of sleep, Boxee is preloaded and I can navigate Boxee easily. When I want to switch to television I simply push the "watch tv" button and the PC goes to sleep and switches to the satellite etc. Its really slick.
The most difficult problem I had to deal with was Boxee loading on windows startup. What I wasn't noticing at first was that when Boxee launched it prevented my storage agent for the NAS from logging in and I wouldn't get all of my shares mapped. I'd go to "movies" in Boxee and only local items would show up. What I had to do was add a -d "x" (where x=seconds) switch to the startup to delay Boxee from starting for around 20 seconds giving ample time for the storage agent to load properly and map all of my drives on the NAS. Once that was solved everything else went pretty smooth.
If you're looking for a MCE remote then I can recommend the Rosewill item I linked as I find it to be a competent remote despite the fact that I dont really use it...and its reasonably priced as well. The remote setup easily and worked right out of the box. The Harmony factor goes without saying. I find it to be the true solution and wife proofing factor that will make my little Boxee project successful. I would expect all of the Harmony line would work similarly. I have 5 devices to control so the 700 was a good fit for me. I can still add one more device so I have a little bit of scalability as well.
Anyhow, hope this information is helpful...if not well at least I'm able to vent my success with remotes here. Great forum...lots of good information.
Acer AX1700 HTPC: Windows 7, Boxee, Nvidia G100(HDMI), 4GB RAM, 640GB HD. ISO/MKV's on Netgear Stora NAS w/2TB. All Gigabit wired ethernet network with 802.11N wireless.