I think the biggest thing you can do is ensure that the home is easy to run wires inside the walls and across floor/ceiling spaces without making a big mess. I recently moved into a new-to-me house and have had to do a fair bit of home automation/network refit. In this case, this is a single story home with a full basement. The basement is finished but has a drop ceiling instead of sheetrock. This makes it really easy to run wires throughout the house since you can run the wires in the space between the ceiling and the dropped ceiling and access the space immediately below any wall space.
Need to run a cable into a new spot on a wall? Cut a hole in the wall, put a data ring in the hole, then use a flexible drill bit to drill a hole through the bottom plate and the subfloor. Find the hole underneath and use the drill bit to pull the wire up through. Simple.
The basement walls are similar as you can access the top portion of all of the walls above the dropped ceiling.
This will also work in a 3 story house as well, just make sure you have a full attic or crawlspace which gives you access to the tops of all of the 2nd story walls.
This helps future-proof the house.
I'd also consider/ensure the following:
1) Make sure there is a NEUTRAL at EVERY electrical box, including switches. Makes things lots easier. I've also gotten in the habit of using an additional conductor from the lightswitch to the light in case I decide to install a fan or similar.
2) Have the electrical contractor use the biggest box that will fit in the wall space. None of these cheap 2" deep things. 22 cubic inches is the size for a single gang box. They are roughly 3.5" deep (the width of a 2x4 wall stud). This is to accomodate the much larger volume of a home-automation switch and/or outlet.
3) Consider truss construction in spaces you'll have to run lots of wires through - it solves the issue with too many holes weakening the structure.
4) Take the advice of others on the thread, and do go ahead and install boxes with conduits on at least each wall. The conduits should be at least 3/4" - 1" would be better. If you've got a dropped ceiling or similar, they just need to be stubbed out into the ceiling/attic area. If you're enclosing, then they need to be run to a central closet or similar.
5) Don't forget satellite, cameras, etc. etc. etc. - run boxes/conduits for them as well.
6) In bedrooms, think about where the bed might be placed and make sure you have outlets on both sides of each bed position. In the master, if you know where the bed is going to be placed, consider adding nightstand height switches and/or boxes for automation controllers, cell chargers, etc.
I probably could keep coming up with other ideas, but that are the main ones...