Brian, these may sound like really stupid suggestions, but my wife and I built a home about two years ago and these are some of the shortfalls:
1. Exterior outlets. I'm not talking about just at floor level, I'm talking about having a couple come out on the side of the house, like on the porch or something, 6 or 7' feet off the ground. A buddy of mine has them on the ceiling of his porch, facing down. Makes putting up Xmas lights a lot easier than running a bunch of extension cords!
2. Make sure you get at least one storage closet big enough to hold a full size vaccum cleaner. I know it sounds dumb, but our house doesn't have a coat closet and we're forced to keep the VC in the garage.
3. Someone already suggested this, but I'm reinforcing the idea. Isolate the crapper and make sure it has it's own exhaust fan vented to the outside. WELL worth the positive impact on your life!
4. Figure out how many outlets you want, then DOUBLE that. Trust me, even then you'll still find yourself wishing you had them in other places.
5. Recessed lighting is much nicer than having to add a bunch of lamps, and it's relatively cheap to do when you're building the house.
6. This might not be a big deal up there in cheese country, but I've slowly added a ceiling fan to pretty much every room in my house, and there's a couple where I wish I could, but can't. At least make sure you have the wiring run in case you change your mind.
7. I got this tip from a contractor friend. In your laundry room, put down industrial rubber floor padding instead of tile or linoleum. Not only is the stuff indestructible, it actually helps isolate the noise and vibration from the machines. There's a lot of different varieties available and it's pretty cheap.
8. If you're going to have a computer in a room and you know exactly where it will go, consider floor-mounted outlets, looks a lot cleaner than running the big bunch of wires down to the floor.