At least 1-2 outside electrical outlets on each outside wall on their own circuts.
(dang handy for christmas lights) or some job that takes a corded tool and not hundreds of feet of extension cords)

2-3 foot overhangs all the way around the house  to get water away from the foundation.

Way Over insulate incoming water lines plan for a 200 year freeze.

An complete fire/ burglar/ monoxide/ monitor(video)  etc.. detection system is cheap without sheet rock. Insurance reductions should pay for system,,  It'd be handy when your lurking on NAT,, front door bell rings and You can switch channels on your computer and SEE who's at the front door !!   (I'd run video cables to ALL entrances and garage area, and a couple for out side walls at the eave line)

TV, cat 5 cable, phone jacks, all the normal stuff...

Always plan for say a wheel chair, etc.. doors-wider halls than normal, shower that can be accessed w/o crawling into a tub-etc. 

1-2 insulated (keep from freezing) water outlets on apposing corners of house with hot water accessable (ever want to wash something in hot water and try to do it outside?)

2 oversized laundry tubs with hot/cold water next to washer drier. (Ever had some really filthy "thing" that needed to be presoaked to get some of the krap off??)

Main walkways (concrete) to house should be NO less than 4 feet wide. handy for moving Large items on dollies into/out of the house, people normally walk side by side and 4' looks proportioned to the house-yard-etc.  Plus in winter time it's easier to use a small tractor blade/ snowblower.

Entrances designed so weather does NOT run down your neck when you enter/exit.

Put in Big enough electrical service so each Room has it's OWN circut and mark them. If for some reason your wife or child has to turn off the electricity in the kitchen cause Dad did "something"  the wife or child only has to look for a switch marked "KITCHEN" or "bathroom" or "master bedroom"  Things like garbage disposal, or refrigerator-dishwasher could be on their own circuts

IF you live in an area where electricity is more of a "iffy" thing, pre-wire so the house can be hooked to "prioritys" and a generator can be hooked up real easy and quick, and disconnected to incoming power (or non-power) lines. 

Just a few things I've thought of...  (you already mentioned the whole house vac. don't forget to run a vac line to the garage (attached garages) handy for cleaning up a "project" or cleaning out the car.