My definition of a green building is one which minimizes costs when all things (particularly externalities) are considered. All other principles spring from this definition. When I say all costs, that includes many things not ordinarily considered as costs. Production of pollution is a cost.
No matter how energy-efficient and ecologically friendly a building is, if it is torn down after only a few decades, it can't very well be called green. There are two components to keeping it around for a long time.
First, most obviously, you need to build well; good materials, good construction techniques, and dare I say it good location (building a thousand year house on a hundred year flood plane is short sighted).
Second, building must be loved. Through beauty or emotions, a building can arrange its continued existance and maintenance.
One of the best and cheapest means of making any building (in climates requiring space conditioning) more efficient is insulation. Insulation is generally fairly cheap and will likely have more impact on your energy bills than any other single factor.
A word about government recommendations: DOE insulation recommendations are based on a number of factors and include assumptions about building construction, and inflation of energy prices. As such they may not be correct for any particular situation. For example roof insulation is generally recommended higher R-values than walls; not because you necessarily need more insulation in your roof, but rather it is easier to put insulation in an attic, than in a wall, when using common building practices. Here is a calculator which allows you to set your own values for the various assumptions.
Siting the Building
Siting a building properly can make a huge difference in how well it performs. The simplest thing is just to make sure that the long side faces south. Next ensure that that south is as open as you can make it. For example if there is a clearing where the building will go, put it at the North end of that clearing. This allows the maximal amount of sunlight through the south windows (in the winter). It also provides an open space on the south side for outside activities. Lawns, patios, porches, are all more used when located to the south of the building.
Other siting considerations include having a barrier of some sort to block frigid winds, block of unpleasant sights, view of pleasant sights, ease of access, minimal disruption of established ecologies, and proper dealing with runoff from impervious areas.
Vernacular design is one built in response to local environmental conditions, and with local materials (usually of necessity). This is a good place to start when designing a green building. Look at the oldest buildings in the area for ideas.
Materials which are shipped from afar, gain embodied energy, that is the amount of energy needed to manufacture, package, transport, install, remove, and dispose of materials. Embodied energy is often used a measure of environmental impact when comparing materials.
A building most adapt to changing circumstances in order to survive. Part of this lies in an overall design which is suitable for multiple different uses. Another aspect is construction and systems which are easy to change.
Passive before Active
Passive systems, such as insulation, earth tubes, and passive solar, are cheaper initially, and throughout the life of the building. Put your initial effort and money into them, and only then consider active systems.
Open building is a concept I first saw in Stewart Brand's book How Buildings Learn. It concerns arranging parts of a building such that those with a short lifetime can be replaced or upgraded without disturbing (or ruining) parts with longer life expectancies. A negative example from my own house, the electricians drilled holes through the timber frame (with the longest lifetime of any portion of my house) in order to run wires which will probably need to be updated in a decade. I had laboriously laid out paths for wires which avoided this, but they did what was easiest for them and what was easiest at the moment. Tedd Benson's work in timber frame open building.
Much attention is paid in recent green writings to reducing the toxic materials used in building. Although this is done to increase the lifespan of the occupants, it also helps improve the lifespan of the building. Sometimes toxic materials are enough to condemn a building. It is easier to tear it down and haul it to a landfill where someone else will have to deal with it. Additionally, materials outgassing toxic substances into the air, increase the need to ventilation, and with ventilation, increase the need for heating or cooling.
The easiest solution is to keep anything toxic out of the building.