We are planning to build a two story house with ~2200 sq ft. in southern PA.  Later, we will add a master bedroom suite on the first floor.  I am very interested in geo thermal and solar related technologies.  What I am concerned about is cost.  I am looking for is ideas on what I could/should include in the initial build out and what other things I could add later as money allows.

What would you do with a clean slate?