You did not specify where you were building the home - North with heating concerns or South with cooling concerns.
In the North I have found one of the best heating methods that is very comfortable and economical is radiant in floor heating with PEX tubing in concrete floors so you get a nice thermal battery and very good heating characteristics.
In the south some of the posts on ground loop heat pumps are very good advice.
Lots of insulation in either case. Radiant barrier in the roof. Living roofs can be very beneficial as well.
Metal roofs can be very long lived, but can be very noisy during storms.
Maintenance free exteriors are also a godsend.
The comment on the higher basement ceilings is also very good, I wish it was an option when I did mine.
Conduit to at least 2 places in each room is also good to a central wiring / electrical room.
Conduit between basement and attic also is something I wish I had done as we added spotlights out back and security cameras, would have made it much easier.
Home automation systems are a nice to have, control-4 seems to be a very good high end system with good support.
Lots of closet space, more than you think you need, bedrooms, bathrooms, attic floors, etc. people tend to collect tons of stuff.
Over sized garage - wider than the cars you tend to put in and deeper - lawn mower, bikes, patio furniture in the winter, kids stuff, and on and on.
The indoor wall sound proofing is also a great idea - we did a little for the master bedroom and bath, but not enough.