1) What should I run in the walls? Our electrician has a fat cable bundle with CAT6, coax, and telephone that he usually uses. I'll probably ask for an empty conduit/loom with a string, so that I can run stuff later.Ah I sort of misspoke - by "everything" over IP, I was thinking: lighting, power control, AirPlay (via AppleTV and AirPlay-compatible receivers), cameras, and a thermostat (although it doesn't seem like the Nest is as hackable as I hoped). I just don't want to keep having to switch between apps - one for lighting/power control, one for cameras, one for Nest thermostat, etc.
So, the big questions that remain at this point:
I'd run 3-4 Cat5e/6 to each room you care about. It's cheap and super flexible (RS485, RS232, Ethernet, HDMI, IR). Run CAT6 to any location you can imagine trying to control something over Ethernet or serial (for example, Sprinklers, Remote ELK modules, Brultech power monitoring, outdoor WiFi, Pool Automation....). Also consider running speaker wire wherever you plan to put a speaker in the ceiling or wall, or outdoors - or if you want to spend big bucks, put 120V power at the speaker locations and use an Ethernet enabled speaker. Put power at any camera locations. Consider running power + Cat 6 to the headers of the windows for automated shades.
Only reason you'd need COAX/RG6 these days is for a satellite or cable box.