Floor heating/cooling/ Far more efficient than forced air and no worries about the crap your moving around your house (mold, pollen, etc.) so fewer respiratory issues. We kept our house in Korea at 17C (~63 F for the US folks) in the winter and would sweat if we wore anything other than shorts and t-shirts. You can also tie into your geothermal/solar for even further reduced costs.
Definitely solar/wind power capability-- as close to "off grid" as feasible in the desired footprint. Tie in to grid but be self sufficient when necessary.
Along the discussion of the DC home, a good inverter and maybe dedicated DC outlets. Maybe just feed outlets directly from solar/wind battery bank.
I'd add switchable glass windows to go "opaque" whenever I wanted, at least in the bedrooms.
Intercom with a console in every room, and one on the back patio/deck and garage. Less of an issue if you are building a single floor house, but quite helpful if you live with folks who are hard of hearing or you're building a reasonable large or multi-story house.
The obvious speaker, network, and coax wiring throughout.
A "dark" room with full faraday cage built into the walls. Turn it into my home theater or something. Nothing in, nothing out. Nice for private conversations and no distractions while otherwise entertaining.
Obviously some of these assume a fairly large budget. The geothermal with floor heating shouldn't be too much more to invest in initially than a "conventional" forced air system, though and will pay for itself fairly quickly. (In the central Atlantic region of the US, my calculations were about 7 years for initial install and something like 11-13 for a retro-fit). Adding solar/wind won't cost significantly less than they would as a retrofit, except possibly the grid tie-in. Do the grid tie-in either way and save yourself some trouble down the road.