Please state the motherboard size you are looking for, and if you have already a processor/other components or you are starting from scratch.
Most mobos I know have IR connectors, that means you need to connect an IR receiver that is bolted on the case. (Quite a few HTPC cases do have one for obvious reasons)
But you can find IR receivers using an internal USB port, that can wake the PC just as well as you can set that in BIOS.
I found more useful the external USB receivers
though, as you can tuck the machine somewhere where you don't see it and place the IR receiver in the best spot.
As for the "I could use any high end LCD remote", I think you cannot. Remotes of different devices send different signals, and it's actually good like that (this is to avoid the TV remote from turning on the air conditioner for example).
You need to use universal remotes like these
that can control the HTPC and possibly the TV as well (depending on what you buy).