After following advice here along with friends, I have decided on the following and respectfully ask for critiques:
-For audio, I want to go with sonos. I will still utilize a bose surround sound system for the main tv/movie room, but other zones will simply have a 5 speaker sonos unit. This eliminates a great deal of speaker wiring and takes advantage of the growing use of wireless.
-I will utilize a crestron system to control lighting, environment, security and possibly sprinklers.
-For each tv drop i will have coax and double cat6 to take advantage of the new directv slim profile boxes. This will also allow me to send hdmi from a central point using converters.
-Every room will have double cat6 drops in two places. I may drop them in many places, but keep them behind the wall instead of plating them all and mucking up the rooms with plates. This will be in addition to security and thermo panel locations which will each have double cat6 drops as well.
-I have a dedicated closet to house all centralized equipment. It shares an exterior wall, so I can install an exhaust fan for temp, and also easily pull in wire from outside.