Rather than start a new thread I figured I'd use this one as my issues are somewhat similar.
I have D*TV which allows you to use either a RF or IR remote. I tried the Harmony units but sent them back... they just don't work well in RF modes. What I'm using for the D*TV receiver and all my current AV hardware is a AR (Acoustic Research) XSight remote which actually works with both IR and RF devices. So far, I've been able to set it up with the online software to control my Mitsubishi WD65737 DLP (IR), Yamaha AVR (IR), Sony BlueRay DVD (IR), DirecTV HR20 (RF), and also my basic Comcast Cable (IR via TV Tuner).
The XSight is relatively attractive, sits in a charging dock, wakes up the minute you move it and lights up all the controls and the LCS screen. Like Harmony, they have an online programming setup which can be a little intimidating, but I should also note they have great phone tech support. Macros can turn on multiple devices so if you want to watch a DVD, you select "Watch a DVD" from the menu and it turns on the TV, the DVD player, and the AVR and most all the DVD and audio controls you'd normally use are available. Supposedly it is the only remote that actually has just about 100% control of a DirecTV receiver including guide, playlists, DVR, etc. and more.
This Winter's project is to get my Gen1 ATV in the AV mix and see if I can actually use XMBC to stream movies via ethernet from a external HDD up to the Mits big screen in my family room. Although it might work wirelessly, to insure better quality I'm going to run a ethernet cable from the Airport to the ATV. Its about 20 feet (snaking the cable) if that and almost directly above me.
The other approach would be to try the iPhone APP. Waiting on the iPad2 as well... but I'm hopeful I can get the AR XSight to do this.
EDIT: 01/04/2010 - Just found out that AppleTV Gen1 is no longer compatible with the latest v.2.1 REMOTE App.