Several people have commented on going passive thermal, good insulation, etc, and really, these are the things that you will value long-term (as well as, by the sounds of the type of person you are, the "hackability" - which is where the often-reiterated conduit comments come in, as that really is your best option - well, any easily-accessible cable run system; I suggested false ceilings further up as another alternative).
If going concrete slab foundation (probable nowadays), put a layer of expanded polystyrene under it. This thermally isolates the house from the ground, and means you can do things like passive solar, using that concrete block as your heat storage.
Of course, if you care about the environment, you are better off minimising soil disturbance, so instead of cut-and-fill as is common now, build around the existing landforms and use piling instead of a concrete slab (a piled house has the advantage that it's potentially more flood-resistant, and it gives you a crawl space that will be very useful for running cables in future).
Some of the suggestions are very region-specific; do you need to worry about pipes freezing? Is it dry or wet where you live? How much is heat or cold going to be an issue? Snow? Tornadoes? Rain? Drought? How much does the local climate affect your design decisions? (e.g. Southern California is going to be quite different to Seattle, which will be quite different to Florida - and these are assuming, like others here, that you are in the USA; something like Norway or Fiji or Egypt would be very different again). Design for the local conditions (e.g. don't make a grass lawn if you live in a desert - that's just dumb, and irresponsible). Local building codes, water take laws, height restrictions, material availability, etc matter a lot, as do things like whether your specific plot of land has covenants on it.
Build responsibly: have a think about the ecological and economic impacts of what you are doing. Look at life-cycle analyses for everything, and if you can, try to get the best score on whatever local "green star" certification system is available (not only will this mean you have a more energy-efficient home, you also minimise environmental impact, and usually - somewhat counter-intuitively - your build cost as well). Recycled materials are great (shipping containers, crushed glass and waste paint in concrete - also can look amazing when polished - recycled wood, recycled aggregate/crushed concrete). Depending on where you are, you might have to do some work to find local suppliers and contractors who will work with (or know how to work with) such things, but it is worth it.
As long as it's not a desert, make use of your stormwater. At the very least, go for a low-impact build (green roof - added insulation as well - or raingardens, or any number of other neat solutions), or simply run it to a tank and use it for grey water (watering the garden, flushing toilets) - or even as your primary water source. A water tank above ground level is harder to build, but means it doesn't need a pump (be creative).
If you are going really crazy with your tech ideas, consider crawlspaces. You probably don't need these in every wall (though the fun you could have with secret passageways should not be understated!), but even just under the house or in the ceiling would make accessing conduits etc easier (also, think about the roof structural design, and whether or not you can actually negotiate it without needing to be a contortionist or a midget). A totally bonkers but awesome idea would be a full-height tunnel that runs under the structure as a "backbone" for all your services - if you're feeling really crazy, this could even go to the property boundary, making service relocations a breeze - and, even the option to check the mailbox in the rain! (I once got a tour of a large auditorium that had one of these running under the carpark, and it was pretty awesome - would be especially so if you have kids). You won't need to care about the walls there lined with pipes - in fact, it would be a good setting if you ever choose to make sci-fi fan films!
Solar passive thermal design and good insulation cannot be understated. Think also about humidity control though - if you have a sealed-up house, consider how you are going to avoid it getting damp (unless in a desert). Use ground-loop heat pumps as they're the most efficient (called "geothermal" by some here, though that term makes me think of this kind of thing).
LED lighting, of course, and the suggestions of a separate low-voltage DC circuit for these. One idea I had a while ago was having all the lighting on a (probably ethernet with PoE) system, whereby each individual light can be controlled centrally. Even better is do that with LED clusters that let you control the brightness and colour (mood lighting, disco, or whatever you want it to be). You'd probably need an Arduino or Raspberry Pi or something at each light fitting (or cluster), so it could get expensive. With that, I figured you have touch panels where you would normally put light switches that turn off and on (to a pre-set default) with a single touch, fade brightness with a sliding touch from the bottom or top, or go to a full-house control view on a long touch that gives more specific control (probably a top-down view of the house allowing control of each room). This would be amazing, but probably too much cost and work to be realistic... LED ropes recessed into the ceiling in an extended architrave is a nice way to add ambient light control.
Go solar. I actually wouldn't advise going off-grid though: feed back into the grid instead - this way, you have a backup if your systems aren't cutting it, and any over-provisioning still nets you money. One suggestion I heard was to have the panels facing West not South (or North) - this is less efficient overall, but gets more energy in the high-demand evening (i.e. shifts the supply curve to more closely match the demand curve).
For water heating, I'm not a fan of on-demand gas systems (you get full pressure and good heat, but they tend not to be useful for small amounts of hot water, or any on/off cycling). Heat pump hot water cylinders are the most efficient I know of (short of solar thermal, or maybe a wet-back log burner if you have a free supply of logs, and the space to build it as a proper big boiler). Presumably you could have a ground-loop heat pump hot water system (GLHPHWS?!?), though I haven't seen these myself (and will not be attempting to pronounce that acronym). Actually, a true geothermal heating (i.e. you live on top of an active volcanic field) is probably the most efficient, but that is very location-specific. On that note, if you have that sort of heat source, then you don't need any other energy source; you just have to hope the volcano risk doesn't eventuate in your lifetime.
Design and build something to outlast your lifetime. Most houses now are built with a 50-year lifespan max. I reckon that (especially considering the life-cycle impacts of construction materials), we should be building for 200 to 1000 year lifespans - however, this only makes sense if your structure is somewhere that isn't likely to get bulldozed in the next few decades. Building to reduce maintenance costs is good though (but it does usually push up your capital outlay in the short term).
One thing you could consider is a modular design: either internal walls that can be easily configured, or interconnected "pods" of some kind (shipping containers are good for this kind of thing) - build what you need now, and expand later if you want. I think one of the keys to longevity is having it able to adapt without too much difficulty.
Soil is a great insulator. Use your imagination (also, having your rooftop as a usable space seems to be a much better idea than the pointy, water-impervious space-wasters of the urban sprawl).
Bamboo is an interesting material I have only recently come across: strong (tension and compression), lightweight, grows really fast, environmentally sustainable. Using bamboo laminate, you can build all sorts of things (google it).
You don't know what technologies are going to go extinct and which will fly, so don't spend too much money on cabling etc - but do make it easy to change. I would suggest you install what you need now, plus likely expansion (e.g. put 2 Cat6 where you think you need 1, but don't run fibre and coax and HDMI and string telephone everywhere unless you can see it might be useful - put it in later if and when it becomes a need).
Some have joked about Faraday cages to keep out the NSA, however the reverse is probably more important to consider: anything that blocks RF is going to kill cellphone and wireless signal, which can be a real pain (we live somewhere with patchy cell reception, and it's annoying). Steel framing, reinforcing, or even joinery can do this, as can anything thick enough. If, like us, you don't bother with a landline any more, this is especially worth considering. It's also a lot easier when one router is sufficient (I once helped someone install wireless networking on a house with a concrete-on-corrugated-steel floor between the levels, and nothing got through that (of course, not even cabling, because of the impenetrability of it, and there not being any convenient ducting).
Fruit trees are great: fairly low maintenance, and you get free, fresh food.
In general, think ahead, and ask around (which is exactly what is happening here). Build for maximising future utility. Exceed minimum compliance and go for well-thought-out, simple-yet-easily-modifiable designs (note that the first half of this sentence is almost a direct quote from an engineering review of buildings in the Christchurch, New Zealand earthquake, so it's about more than insulation). Tech dates quickly, so don't spend too much tying yourself down to one thing.