ZigBee
Comprehensive standard (IEEE-ratified) for home automation, energy management, etc. Unfortunately, the "standard" does not appear to let devices be interoperable with equipment from different vendors.
Getting ZigBee equipment seems difficult: you have to resort to eBay, or deal with dealers with extremely high markups. Cannot order equipment cheaply or easily.
Largest vendor in the space appears o e Control4.
Z-Wave
Controllers
Mi Casa Verde Vera 2
Runs Linux and OpenWrt? Free (no monthly fees). Web UI, accessible through company's website.
Linux Journal has a review of the Mi Casa Verde 1. Yes, that is a bash script controlling the lights.
TrickleStar 300ZW Z-Wave Dongle
Cheap. Appears to work w/ Linux. Amazon
Devices
GE On/Off switch. Amazon.
Trane thermostat. Amazon.
Software
open-zwave. C++ library for interacting with Z-Wave dongles/etc… seems very basic still.
Stores
HomeSeer has a large selection.