We will build about 2500 sf house in Auburn, CA, just above Sacramento. I think it is zone 3, Mediterranean climate, warm-dry summer, 30 degree lows in winter but not often. Topography forces house to face east on a north-south axis, so passive solar has less impact. What software do you recommend to help determine levels of insulation, windows, placement, etc? I will shade east windows as much as possible, add as much south windows as possible. Unfortunately, main living space must be on upper floor, with bedrooms in daylight basement.

search DANA1 and read other threads for some info.

DOE2 or BeOpt are pretty good freebie download energy use models that take site factors and weather data for US locations. (BeOpt has DOE2 running underneath, but has more features.) See:

http://beopt.nrel.gov/

http://doe2.com/

What makes sense economically varies with heating fuel type. If you're on the gas grid & or next to a big hydroelectric generator it skews things one way, compared to propane, heating oil, or high-priced electricity only as options.

Summertime dew points in Auburn CA are comfortably low, and overnight temps reasonably cool- you may be able to use a night-time ventilation strategy for most of the cooling in that location in a high-R house.

http://weatherspark.com/#!dashboard;a=USA/CA/Auburn

Wintertime average temps are also high enough that (relatively) low cost ductless air source heat pumps ("mini-split" or "multi-split") would be as efficient or higher efficiency than ground-sourced "geothermal" solutions, and can provide both heating & cooling, consolidating system costs. With a reasonably high-R house with decent heat-rejection designed in, temperature differences between rooms can be minimized even with the active ductless heads in the larger open spaces. These deltas can be improved further by using heat recovery ventilation (HRV) with the exhaust registers for the HRV primarily in the rooms that don't have the heating/cooling head for the ductless, putting the ventilation supply registers in the open common spaces with the head. With some careful forethought & planning it can usually work with one head per floor- I've even seen a non-superinsulated 2-story home with 2-story great-room that manages very comfortably with a single head.

You can use the generic cook-book approach as a starting point for whole-wall R values on your BeOpt modeling. See Table 2, p.10:

http://www.buildingscience.com/documents/reports/rr-1005-building-america-high-r-value-high-performance-residential-buildings-all-climate-zones

Note that those are whole-wall, not center-cavity R values. An R20 wall (recommended for US climate zone 3 in the table) would be a 2x6 framed wall with cellulose cavity fill + 1" of rigid polyiso sheathing over the structural sheathing as a thermal break for the framing. An R20 batts or cellulose filled studwall without the exterior insulation comes in at R14 with the thermal bridging of the framing factored in.

There's a federal direct subsidy for U0.20 windows among participating vendors that may be worth considering for the east, north and west facing windows, but the south facing windows should all have a higher SGHC for so a U0.35-0.42 clear glass may be best there.

See: http://www1.eere.energy.gov/buildings/windowsvolumepurchase/