Have you looked at the current crop of iPad/iPod remote apps - such as iRule, Roomie, DemoPad, etc.?
You can easily couple any of these, via something like a Global Cache converter, to a wide variety of whole-house controllers.
FWIW, I use Roomie on an iTouch, to a Global Cache GC-100 to control my B&K CT600 via IR. Response time is ostensibly instantaneous, and the connection is rock solid.