I'm in the planning stage of the same kind of house that you are planning on.  If you PM me I'll send you some links for some interesting sites dealing with homes and energy efficiency. 

Take a look at pathnet.org, under "resources" click on "Tool Inventory" and go the area you are interested in.  You will find a lot of information describing the technology, manufacturers and results.  They do not list every manufacturer so you still have to search but at lest you know what you are looking for. 

Some of the more interesting technologies at pathnet are combined heat/cooling power units, alternative septic systems, solar lighting via fiber optic and heat pump water heaters.

Consider adding a residential fire sprinkler.

Consider PEX for plumbing.

Go to http://www.dsireusa.org/ for a list of federal and state energy incentives.  You may find that solar is a little more affordable.  Take a look at wind as well www.awea.org  or maybe micro-hydro if you have the water.

I’m planning on a whole house battery UPS system that is tied into wind, PV and a small generator total is estimated at $15-18,000 which is a lot cheaper than having seperate sytems for PV and wind then adding a standby generator.  Try outbackpower.com or xantrex.com. Take a look at bannerpower.com but they are extremely pricy for what you get.   I’m working with one supplier in MN www.backuppowersource.com to get everything connected while minimizing cost.

As far as Geo thermal go to the Geothermal sub forum on this site.  There are a couple threads that are well worth reading.

You didn't mention the most important feature of your house.  What type of construction is it going to be SIPS, ICF, stick or something else.  FWIW we are going SIPS with precast foundation.  Go to the subforums here for more info. 

Graywater or Greywater search on both spellings.  I've run across a number of sites dealing with the subject.  http://www.towtrc.state.tx.us/common/GraywaterLiteratureSearch.pdf

If you have the land and trees consider harvesting trees that are going to come down anyway and find a custom sawmill, kiln drying and milling operation that specializes in small batches.  I have and will be getting quarter sawn sycamore and red maple and plank sawn hickory and white oak for flooring, cabinets and trim for $2-3/board foot.  Not only is it cheaper but it ties the house in to the area nicely.

Mark,
   My 1st priority(and should be for most others) is to Super Insulate. When you reduce your Heat Loss/Gain, you are already way ahead of the game. It also reduces the amount of energy required, and thus minimizes the importance of your mechanical systems. Sure efficient mechanicals are important, but if you are only using 25%(or less) energy than your neighbor only so much more savings can be accomplished.

   Start with Super Insulating, and everything else becomes a bit simpler, and your other paths easier to choose.

Good Luck! 

For example, lets say I put in a MCHP system for hydronic heating. What is more efficient at this point for hot water? An 80 gallon hot water tank or an electric on demand water heater? In the winter time I can see that the 80 gallon tank would probably work out better because the energy from the MCHP will constantly keep it at a moderate temp. However how much EXTRA electric energy in the summer will the tank use to maintain temperature when the MCHP is not running? Better yet, do I take it a step further with some electronic change over solenoids that switch off depending on the season? I probably won't go with a MCHP anyway, but these are the kinds of questions that finding the answers to without making a decision first to find out the result later are hard to get answers for.

You’re right to consider how everything in the house connects, you could save a lot of money by not buying systems that don’t work well together efficiently or effectively.  Make a master plan of what you want and build accordingly.  We are including the infrastructure for systems that we may not have installed right away because of cost or we think technology will change in the near future.  For example I haven’t found a grey water system that satisfies our requirements but we are still going to install a dual drain system and allow for room in the basement for the system.    

I’ve looked into the MCHP and for on grid use I don’t see the advantage, it is a good ideal for some situations.  You still only get 85-90% efficiency out of your fuel and the units are not cheap.  Why not just buy a 90-94% efficient heater, it is a lot less expensive and the install would be less expensive as well.  I think MCHP makes sense for remote sites or for back up power if you have a battery system but not the typical on grid customer.  I’m trying to find a stirling engine that would connect to a wood fired outdoor furnace that will be used to heat the detached garage and snow melt systems.  No luck yet.

Take a look at ground source/geothermal and consider a superdeheater for the hot water.

As far as on demand hot water.  I think they are great, but they are not the solution for every situation.  We originally were going to install them in the new house but after reading about  how they operate most effectively and mapping out  our requirements and the other systems we realized that  on demand would not be the best solution for us. 

I'm actually leaning towards geothermal for heating through hydronic. Can hydronic be an effective cooling option as well?   

Search in the geothermal forum, I believe the answer is no, but there have been several discussions about that subject.

As for the other major energy contributions, I was considering a change over inverter system based on a natural gas generator, some solar panels, and batteries. Perhaps with something like the GridPoint system.

That is what I’m looking to do with the Outback system.  Just a quick look at GridPoint I don’t see any provision for 240 volt which would be needed for your ground source heat pump.

You really want  to do a life cycle cost analysis on that NG generator, very expensive to feed vs gasoline or diesel.  I only know about the outback system, but if the generator is running the power by passes the batteries and feeds the house directly.  So if you have voltage/cycle sensitive equipment like computers you need close to utility grade power.  I’m planning on using a Honda EU series generator with a automatic start controlled inverter/charger.

Other things I've been thinking more about are size.  I like to tinker so I need some extra garage space and my wife and I would like a shared hobby room somewhere in the main house.  I'm thinking I'd like to have a 3 stall garage that has an extra 10 feet or so in front of the parked cars for 2 stalls and the third stall is just deep enough for a car and probably small enough that getting out on the wall side would not be possible once the car is in the stall. .  That said I'd like to keep the entire living space in the 1500 sq. foot range. 

Consider excavating under the garage for additional space.  My architect said the cost is very cheap because you are having to make a structural floor for the garage anyway.  Most of the dirt has been removed to build a ramp for the equipment and crews to get in the basement for foundation and floor work, then the dirt has to be put back and compacted before the garage slab is poured, so you pay to make a hole then pay again to fill the hole.    As long as you are sinking a lot of money into the foundation and floor for the garage why not excavate under the garage and get some cheap space that way?   Depending on the orientation of the house and land terrain you could even have a footprint of 1,500sf and put the garage in the basement.