The Plan #119-1232 (DDI105-202) has some major green advantages and opportunities. To start off with, its basically a three story home, which is not only less expensive to build than something spread out, but disturbs less ground. Its many windows and outdoor decks allow natural cooling and ventilation. Perhaps most important, it fits a lot of house into a small square footage. The size of homes has basically doubled in recent years, so a small house that works extra hard for you is a great start!
What can you do to make it green? Well to start off with, think insulation. This plan has a lot of windows and they're spread throughout the house. Passive solar is not an option and windows represent a weak point in a home's insulation. Look into a soy based spray on insulation. You'll get a tight seal around your entire house, and you wont have to worry about harmful VOCs. Other green options are total fill-in insulation, formaldehyde free batting, and other recycled batting insulators. No matter which you choose, remember to seal those air gaps.
Window selection goes right along with insulation for this home. Remember, windows are a good thing, but they dont insulate as well as a wall. Green windows will have a low U-value, low-e glazing, and an aluminum or wood frame. Vinyl frames perform well, but the material itself isn't good to the environment.
A home like this, especially a craftsman house, is just screaming for hardwood floors, stone masonry and tile, plenty of trim and crown molding, etc. Look for locally produced goods of this nature. Try FSC certified or reclaimed woods for floors, trim, and molding. Low or no VOC paints and varnishes will be important for keeping your air quality high. Energy and water efficient appliances are also key.
For this home your focus should be local materials, healthy materials (pollution and air quality), sustainably harvested woods, and energy efficiency. Stick to that and you'll end up with a healthy home that respects the environment that inspired it.