I'd want a single closet/small room where I could put all the equipment for the media/entertainment, cable boxes etc. Then use IR extenders or better yet, one of those wireless remote control systems.
I'd do speakers in the ceilings/walls of most every room/area with zones and volume controls in them. Depending on the square footage, you may need multiple receivers to make it work nicely where everyone can listen to different tunes. Also, outdoor tunes have to be available too.
Wire the house for both wired network and of course wifi. Depending on budget and size of the house, fiber would be nice for at least interconnecting sections of the house.
Along the idea of the wireless remote system, turn an iPad into the house controller. Make life as easy as possible, something you could hand to your grand/parents and they would be able to push buttons and make it work. I have seen systems like this and drool at how nice it is, and it isn't like it is crazy expensive. No more 4 remotes or a "single" remote that works 95% of the way but takes a small training session to even turn on the TV.
Network drops everywhere. Even in the ceilings of major rooms. 802.11N is great, but nothing trumps Cat5E over fiber.
In wall (or ceiling) speakers. atleast 1 in every room, 1 in the 2nd floor hallways. All with volume controls. All wired to a central network closet with multiple Airport Express inputs so the wife scan stream 1 music to the bedroom when shes dressing, and I can stream another station to the family room while I'm waiting.
Network closet should span 2 floors with future pipes into the attic and into the basement for new drops. Network closet is preferably close to the main family room TV for major components. Switches, routers, firewalls (i was a sys admin in a past life) can all go in here. Money willing, put network equipment in 2nd floor closet, tv equipment in first floor closet.
Integrated speakers (mostly in the bathroom, but through out the house and independently controllable would be nice).
This one just came into my mind today, but having a weather proof mic outside would be amazing, especially in conjunction with the built in speakers. I would love to have a natural rain/thunderstorm/birds played throughout my house (echoed from outside). Sure, windows are great but how often can you actually have them open.
* Lighting
* Heating
* Locks (windows & doors)
* TV
* Music
The one other primary feature I would want is an instant facetime type setup between each tablet so that you can communicate with others in the house without having to shout or get up off my lazy arse.