I hate to be repetitive, but I will be anyway LOL. Please keep in mind, I'm no contractor and some suggestions may just be dumb LOL
A large pantry with room for a freezer, and maybe even an additional 'fridge. We use both of our 'fridges and as much as I love the convenience, the extra is in the way. We currently have it sitting in front of one half of the sliding glass door, so it blocks the additional light it could bring in. It's an eye sore, but there's no where else to put it. Most of my extended family members use 2 'fridges and sometimes 2 freezers of a good size.
Maybe have access to the root cellar from the pantry? I would love a root cellar.

Or just make it all in one/combo deal - maybe have a seperate section of it that could be used as a tornado shelter.
Tons of storage is something that's needed through the entire house. Places to squirrel away the blankets, coats, and jackets that you aren't using in the summer. The broom, dust mop, mop, hand broom, dust pan, step ladder and cleaning supplies need a seperate home as well to help keep them out of kids reach. Linen closets!!! If you have large or walk in closets in the bedrooms, you could store sheets and the like in there, but you need somewhere to put the towels, TP, shampoo, soap, shaving cream, extra razors etc, etc. I shop whole sale and I love the money I save, but it gets full pretty quick under the sink...and a basket against the wall for towels is a pain.
I would love to have combination wind and solar heating. We don't get enough of one, so would have to incorporate them both to make it a more self sufficient set up. Maybe you could install a "starter pack" of some sort? ..and the home owner could complete installation if they choose - you supply the parts maybe, or you could at least provide the option? That way, building the home would be less expensive and they would be more likely to buy and feel more comfortable with the set up started, but feel good about saving themselves a little money by completing it.
We currently have an outdoor furnace that heats our water and home all winter long. It's fabulous and I love it. Maybe you could partner with a dealer to be able to offer this option on your homes.
http://www.heatmor.com/ It's not the exact one we have, but it's very similar. I believe they have come out with an attachment that you can hook up to the dryer so all the dryer has to do is rotate - the heat comes from the fire - no smokey smell. A great thing on rainy/super cold days when hanging out the laundry really isn't doable.
Er... A good size clothes line! Something where I can wash sheets and bedspreads and be able to hang them properly.
A large kitchen with oodles of counter space and storage is essential. I thought we had one big enough when we bought the house, but we have VERY quickly outgrown it as we have become more and more SS. I absolutely despise the space we have between the tops of the cabinets and the ceiling. Sure, it's cute for decoration, but the dust and grease really tend to accumulate and cleaning it is a pain in the behind. I have to crawl up on the counter tops .... not pretty. Maybe make that space for additional storage of things like the canner, water bath, food mill, ball jars, cherry pitters, shellers etc.
Built in gun safe? I noticed a few years ago, there was a trend to "secret rooms" in construction. I even saw a few plans that offered it. Might not be a bad idea. Maybe put the gun safe in there?
What about offering an option to install a butchering station? Let them pick the equipment maybe? and you install? Might not be feasible...
or maybe just have a good stainless steel island where the butchering could be done? I think being able to wheel it out of the way would be a good idea, but also think that having a stainless steel island with a sink and running water would be ideal. Maybe offer a butcher block option if they don't like stainless steel.
I agree with nothing textured. My counter tops and floors are textured and it is a lesson in aggrevation/frustration/anger management trying to keep them clean with kids in the house and a hubby who won't take off his muddy boots.
A utility/mud room with a large sink.
Something with at least a crawl space for easier repairs.
I saw a few years back where, on one side of a house it received direct exposure to the sun and the other was completely shaded. You could stand at one end of the house at the window and look out the window on the other side of the house. Opening both windows provided a good breeze because to the temp differences on the opposite ends of the house.
Somewhere to set out and start growing my seedlings in the spring without having to install grow lights or build an expensive green house.
When we bought this house, a big selling point with us was the kids rooms were on the other side of the house with their own bathroom.
Natural light! Overhead lights are EVIL LOL.
Ceiling fans
A wood stove big enough to cook on if the power goes out and someway to block off the room that it is in to trap the heat if it's necessary.
Hard flooring of some sort.
Great insullation in the walls and ceilings. Not just the stuff that is required to bring it to code, but something that is actually going to be cost effective for the homeowner. - like mom2bbjandag said.
One story. DH has bad knees and we aren't getting any younger. Also less of a falling hazard for the kids.
I don't necessarly want to be close to town, but at least with in a reasonable distance to a country store/gas station.
We have 3.6 acres and are quickly realizing it is going to be crowded with all the fruit and nut trees we want to put in and have a big enough space for a large garden, chicken coop, turkey coop, duck coop - the runs that go to each, along with the berry beds. I think ideally, we would want at least 5 acres and have the house located where I can't see my neighbors and they can't see me, but they are still close enough that we could help them if they needed it.
Maybe have double paned windows with blinds in the middle? That way, the blinds won't get damaged or be in the way and stay nice and functional - but still be practical by being able to close off the east facing windows in the summer to help control the temps.
A screened in porch in the back yard with a large ceiling fan.
The dining room only gets used on the rare occasion we get company - maybe once every 6 months - if that. It's currently my sewing/storage room.