Not sure how possible this is, but it seems like it should be possible.
I have a Harmony remote control, which is great for emulating any other remote control under the sun. When controlling the AppleTV and Boxee, though, there are still only 6 active buttons.
It would be REALLY cool if Boxee could make AppleTV accept additional buttons for control. For instance, then we'd be able to have an 'instant pause' button in addition to the 'bring up play controls/select pause' double-button pause of today. I don't care WHAT button lexicon Boxee adopts (although it should also include support for the Apple Remote controls, obviously), as most universal remotes out there should be able to emulate any extant button set without issue.
Overall, not sure if this is so much a "Boxee" realm of device support or if I should be bugging the patchstick guys. But, better remote controllability on the AppleTV would really make Boxee a dream system!