I've been thinking about this a lot lately as I've been trying to make a decision on my approach. I've talked to a few of my friends that are active in the home automation space, and I think I've settled on the idea of using a well-known protocol for my wireless endpoints. One thing I would really like to do is to use UL-approved endpoints that look like they are part of the house, rather than having add-on adapters. I'm exploring Z-Wave and looking at endpoints that natively use the protocol: http://www.amazon.com/Cooper-Wiring-RFTR9505-TSG-Wireless-Resistant/dp/B004SC3GKM
The challenge, however, is figuring out the best way to interface with either the endpoints themselves directly, or to integrate with a controller. There doesn't seem to be an existing Z-Wave shield for Arduino. So I'm leaning towards integrating with an off-the-shelf controller and using the Arduino as a "controller of controllers".
At any rate, as I move forward, I'll share what I end up doing on the forum.