Wood – season firewood over the woodstove

For central A/C, you'll need ducts and vents. Once you have the ducting in place anyway, you might as well use it for both your heating and cooling.

For a three floor house, you definitely want some kind of zoned system, with a thermostat on each floor. (I wish my 2-floor house was zoned.) You may want multiple cooling systems, or maybe one system with motorized dampers to control airflow to the various floors. Your HVAC contractor should be able to make a reccomendation of what will work best.

Whatever you do, do not skimp on the ductwork. Your HVAC contractor should run calculations on how big the ducts need to be. For many home builders, HVAC is a minor concern in the bulding plan. Make sure everything is sized correctly. Changing ductwork after the fact is very difficult. And if you don't have proper ducting, it won't matter how good your central heating using is.

For new construction, Geothermal is usually a good candidate. It can provide heating, cooling, and hot water with crazy efficiency. The installation cost is MUCH higher though. (There are tax credits that will offset some of the cost.) If you aren't up for geothermal, I would go for a traditional air-sourced heat pump for your heating and cooling needs. They are pretty efficient (at least in moderate climates). You are pretty much in the perfect lattitude for a heat pump.

However, I would not have the heat pump (air-sourced or geothermal) as your only heating system. Some kind of alternate (non-ducted) heat source would be a good idea. Heated floors, gas fireplace, etc. Air-sourced heat pumps lose their efficiency in very cold weather. And it can also be nice to have gentle air convection, vs a duct that is blowing in your face. You also have a backup system in case your central heat fails.

That said, ducted air is nice, because some regular circulation of air in all the rooms of the house avoids that "stagnant air" smell, as well as cutting down on dust, dander, etc.

Also, central air systems give you options for humidification and de-humification of the whole house. Look into that. It is usually a minor cost increase in the system, but can make a major difference in comfort.

You have to use double walled pipe when going through walls and floors and what not because the double wall and the space between the pipes cools enough that it can come in contact with wall materials. Single walled pipe would get hot enough to ignite the surrounding materials.

Also, a lot of fireplace type units use a 2 walled pipe that brings in air for combustion through the outside pipe and exhausts hot air through the inside pipe, but that wouldn't be used in conjunction with single walled pipe.