Hire a real architect. It will make a HUGE difference in the usability of the space and the ease which with the contractors can do their various jobs. It's worth the extra money.
make the framing contractor use the best practice plus framing techniques. Or whatever it's called, they can do a better job if you're willing to pay a bit more and it means less drywall cracking and other problems as the house ages, not to mention superior strength in the wind and storms and such. Hurricane strapping? if you're in that area.
After the foundation forms are in place, but before they actually pour any concrete go around with the plans and a measuring tape and be sure they are correct. You can't change the foundation later and you'd be amazed how many designs have to be altered later cause they used the forms they had on the truck rather than go back and get the correct ones to actually build the house you designed. My mothers walk in closet became a regular closet because they used a form that was 3 feet too short!
Dont let the HVAC contractors use "rule of thumb" techniques for calculating how big a furnace and AC unit that need. If the company can't do a manual-J and manual-D calculation to figure the actual heat load and necessary tonnage of AC and BTU of heat, then you dont want that company. Those documents will give them sizes for ductwork, get a copy of the specs and make sure what they are putting in is the same as what you signed in the contract. Flex duct is much cheaper to install and can be done properly and create a good system as well as regular tin, but it has to be done properly. If they get done and it looks tangled, crimped and just messy, then it's not going to work. Complain, get someone out to fix it. A bad AC system is a HUGE problem once the walls are up! DO NOT let them run the AC while doing the drywalling! That dust will permanently clog the coil and the AC guys will need to pump the system down, cut the lines and take it outside to clean it at your expense. If you need to run the heat or AC during the rest of construction make absolutely sure that you have good filters in place and change them every week or so yourself. Nobody else will care to do it but as much dust you keep off your coils the better it will work when you move in. After they deliver the air handler and AC compressor, go out and read the model numbers and make sure they are what you ordered. A lot of companies will isntall a slightly mismatched coil and compressor if thats what they have handy or even feed you a line about better humidity removal or some such. But dont buy it, get a matched system for the best efficiency. If you decide to go for a 2 stage system (which is an excellent idea but is more expensive) dont let them put a single stage thermostat on it! I can't believe how common this is and you are basically throwing away the extra money you paid for the 2 stage system! Make sure.
Tell the electrician absolutely no back stabbing. You want pigtails and wirenuts and no cheap dangerous passthrough backstabbing of outlets. Then be there for the inspection and make sure that they didn't use any backstabs. it's cheaper and faster to install with backstabbed connections, but they burn houses down, not to mention just nuisance failures, burn outs and brown outs. Run a neutral into every switch box, not just a switch loop. Fancy remote controlled light switches and other things that you might be interested in the future require a neutral in the box to run. It's not much more expensive to do this now, but virtually impossible once the walls are up. Run 3 wires (and ground) to every ceiling fixture so that you can put in a ceiling fan later, even if you dont think you want one now. Code says no more than 6 feet between outlets, but thats a maximum spacing, nothing says you can't have them closer together. In office areas or where you think you might put desks have them put in dual outlet boxes so that you dont need as many power strips and various other things later. Put in a whole house surge protector as everything has a computer in it now days, even some toilets
$200 for a really good whole house surge protector is a lot cheaper than buying more and more $30 power strips for the rest of your life. More lights and fixtures is always better. If you put them in you dont have to always use them, but when you want to make it bright, if you dont have them you'll be in the dark.
as far as other wiring is concerned, the more the better. at least 2 runs o coax to every room, maybe 3 if you want satellite and broadcast tv capability. At least 2 runs of CAT5 (or cat6 even better as it can carry video signals too) into every room. I would probably run twice that about of cat5. It's not expensive and you'll have a hell of a time fishing more in later. Dont know about the fiber, can't do much with it right this minute but it's not expensive either so it might be worth it for future proofing. You definitely want a "data closet" where it all ends up so that you can path phone and network and anything else throughout the house. In addition get some long PVC pipe and put in at least one run from the closet up to the attic and down to the basement and you'll probably want to use some PVC to connect the attic and the basement or other such places for you to more easily fish more wires through later.
Lastly get a video camera and go through and video tape the entire content of the walls before they drywall goes up. That way you'll know where that plumbing stack is or where that CAT5 pull goes. You can pull these low voltage wires yourself.
But I think the single most important thing is to just be there while construction is going on. No general contractor can double check as well as you can since you're much more interested and not going to let them do the same stupid things they do on every other job to your house.
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