A couple of things I wish I'd done (not home automation related).
I had them pour a sidewalk from my driveway/gate down the side of the house to the backyard. I should have poured a slab for a future natural gas generator and had the electrical pre-plumbed for said generator.
I would have been king s*** of the 'hood if we'd had that running during snowmaggedon.
Don't forget the height of your garage doors. Standard is 7ft (i think) but bumpt it up to 8 if that is an option. Then you never have to worry about whether or not a future tall vehicle will fit.
Re: a media closet - we did this and wired everything in the house to that central closet except for the media room, which houses its own receiver and the speakers run do it. The network cabling however does go back to the central closet.
in your media closet, in addition to having an HVAC return, put a solid floor down, whether tile or wood or even linoleum. Then your racks can be on wheels so you can easily roll them around to monkey with wiring and components. Along with that, make sure the wiring company provides extra slack in the wiring. Even if I'd thought to put tile on the floor so I could role my rack, the network cables don't have enough slack to move more than a foot or so further away from the wall than they already are pulled. Edit to add - unless you can build the closet in a manner that you can walk behind everything easily. We re-appropriated a bedroom closet for a bedroom we knew we were goign to use as a gym, so its not big enough to do the walk-around thing.
We wired for 5.1 in our family room plus a pair of speakers in the kitchen (its just 1 long room). Then we can play the audio from the tv in the 5.1 and use the kitchen as zone2 on the receiver to play the same. If you plan on putting your sub in the middle of the room (ours is behind the couch) run a dedicated sub wire as part of your pre-wiring. So freaking awesome to not have to deal with wireless transmitters and whatnot, and the great bass is centrally located in the large room.
Overpower outlet your media closet - add multiple outlets. Get a dedicated circuit so you don't have to shut it down, kiling your home audio and internet, when you kill the power to the room to hang a ceiling fan.
I ran 2 pair of speaker cables to the back corner of the house (outside). That was great because we installed speakers around our pool and a subwoofer in the flower bed up against the back of the house last spring. I didn't have to pay anyone to run speaker wire from the media closet to my backyard.
Plan on putting in a pool? Add the electrical now. Want to put infrared heaters on your patio? Add the electrical now (they take a lot more juice than standard lights/fans).
If you're building a 2 story home, triple the amount of time you've thought about wiring on the 1st floor. Any thing after the fact, unless its a room that doesn't have a room above it, is a massive PITA to add wiring. If it's a 1 story home you'll always have attic access to drop wires.
I wish I'd added insulation to more interior walls. Since our home is almost all wood or tile, everything echoes. Any insulation you can add will help. Unless it is a high end custom builder, they're probably only insulating the exterior walls and maybe your media room.
Lastly - if it doesn't come w/solid core doors, just pay the upcharge. It is absolutely worth having solid interior doors. You can't express your anger by walking out of a room and slamming a hollow core door. THey just glide closed unless you keep your hand on the handle the entire time to pull it. A solid door F'ing THUMPS and everyone knows you mean business
