Rough in Tips for Geeks

Having done a lot of home "improvement" I've slowly built a mental of lists of things I wish I (or the previous owner) would have done when the house was built.  These are mostly centered around electronic or electrical stuff.   This is a gathering place for them.

1. If you're ever installing any ceiling boxes in the middle of a room, even if you never plan on installing a fan there, install a fan rated junction box and supports.  Run 3 conductor (3 plus gnd) wire to the light switch.  They only cost a few dollars more up front.
   
2. Prewire for an alarm system.  Run 2 conductor wire to all doors and windows, and Cat 5 or 4 wire cable to a spot near the main entry doors.  I recommend installing the door and window magnet sensors now, since they are easier to install before the trim and walls go up.  If possible pull a 18 gauge 4 conductor wire to a junction box on the front of the house under the eves and up high enough that a ladder is required to reach it.  This is for a siren and/or a flashing light.  You may never choose to install an alarm, but the prewire will cost only a few hundred dollars and will save hundreds if you do.   
3. Conduit/smurf tube - If you have convienent place to run wires like an attic, consider using conduit to join the receptacles on at least the outside walls and run back to the attic.  Finishing wires through fiberglass batts is difficult and nearly impossible with other forms of insulation.  Have a few empty junction boxes in each room with conduit back to the attic for TV or communication cable)  Which leads me to:
4. Existing exterior walls:  Spray foam insulation.  Icynene is one type, though there are others.  These foams are sprayed into cavities and expand to fill the volume.  They are also strong adhesives, so they stick and seal all of the openings and actually add strength to the wall system.  When you are done the wall is nearly airtight, and the foam won't settle over time.
5. New Exterior walls, consider building any new wall systems out of Structural Insulated Panels.  The EPA estimates they insulate about 15% better than a stick and frame structure becuase of the lack of wood studs acting as thermal bridges.  They are fairly easy to install, so in most cases their higher cost is offset by reduced labor.  They pay back in terms of energy and noise resistance.
6. Attic insulation.  If you choose the spray foam, have them spray the underside of the roof deck and gable walls and do not insulate the attic floor or ductwork.  This brings the attic into the conditioned space of the home.  The cost is slightly higher, and it only pays back if your duct insulation is poor.  However, if you ever need to access the attic to run wire, or remodel not having to swim thru fiberglass batts on the floor is well worth the price.
7. Don't "deadend" light switches.  It is a common practice to bring power to the ceiling box, then run a single 2 wire (+gnd) cable down to the switch.  The hot wire brings power to the switch, and the white wire gets remarked as a second hot and carries the now switched signal back up to the light.  This means there is no neutral wire in the switch box, so many models of home automation light switches will not work.  Either run a 3 wire plus ground, or run power to the switch first, then onto the light.
8. Ground Source/Geothermal/GeoExchange Heat Pump - Instead of an ugly noisy unit outside, a long loop of black poly water pipe is buried in the ground, either in long trenches or in wells.  While running as an air conditioner, dumping heat into 65 degree F ground instead of 100 degree F air a GeoExchange unit is about 3 times more efficient.  During a heating cycle, pulling heat out of the ground and warming the house it is about 5 times more efficent.  The wells/pipe can double the price of the install, and as a remodel require making a mess of the yard.  Doing it when the home is built means the cost can be rolled into the mortgage, where it will pay off in energy savings in a few years.  The tubing is very durable, and should last 50 to 100 years.  The central unit being completely indoors also tends to outlast exterior AC units.
9. Consider PEX plumbing, and a "home run" style plumbing system.  Copper pipe was expensive, and required a lot of soldering and couplings to install.  Plumbers tended to run a trunk line that branched at every faucet.  This means it took a while for hot water to reach the faucets (since it had to fill the big trunk line first).  Pressure drops from upstream faucets being used would lead to scalding/freezing showers.  There also tended to be only a few valves in the system, so it could be difficult to isolate a section of piping for repair work.   PEX is a flexible plastic pipe.  Its strong, but can be bent around most corners and therefore can often be installed with no fittings except those at the ends.  There are few chances for leaks, and the lower cost of the pipe means each faucet can be run back to a central "circuit breaker" style manifold in a central location. This makes it easy to turn off faucets for repair work.   
   
10. Have a "mechanical" room.  Set aside some space for the mechnical systems, ideally centrally located.  The room does not have to be exceptionally large, 4' 8' may be enough. This will be an ideal place for the water heater, plumbing manifold, circuit breaker panel, furnace and any automation, communication or security equipment.  It should have access to the attic, or have large conduits run to the attic.  Cover the walls in fire rated plywood to give a nice strong surface to screw everything to.  The electrician will want to install the main panel outside, but just install a disconnect panel outside, with enough room for the breakers required to install a solar system.
11. Install a fairly large subpanel in the garage, with plenty of empty space.  You'll end up adding outlets.  Make sure its a 75-100amp panel if you ever plan on owning an electric car.