In case anyone needs to know, the Logitech Harmony One universal remote works beautifully with the Apple TV. I got the Harmony One as a birthday gift. The Apple TV was in the database of devices and there was even a pre-programmed activity to control the Apple TV. The setup couldn't have been easier. The Harmony software (version 7.6.0) is a universal binary and is Leopard compatible.
I just hit the Apple TV activity button and the remote turns on my HDTV and selects the input for the Apple TV, turns on the Apple TV itself, and away we go. It just works.
Aluminum 24" iMac (2.8Ghz Intel Penryn), Mac OS X (10.5.8), Apple TV 2.3.1 / Sharp Aquos 46" HDTV