Disclaimer - Im an old house buff and biased heavily to traditional styles.
I think we could learn a lot by looking at how homes used to be built when wood was the only option for heat. Small footprint, good southern exposure, small window to wall area, low ceilings, etc. About the only thing that dosen't make sense anymore is a lot of small rooms with doors (good for heating just the in use room with fireplaces, bad for a central stove).
joutl, I think you were right on with the idea of minimizing wall to floor area... but you contradicted yourself later with the one level recommendation. Modern single story construction - ranch homes - are actually the worst deign layout in this regard. Multiple story design is much better optimized for minimizing exterior surface area, the turn of the century "American 4 square" cube is probably the ideal in this regard.
If I look back I think one of the best designs ever from a heating perspective might be the center chimney Saltbox. With proper southern exposure you have a nice wall of windows on the south side to make the most of solar gain, and that long sloping roof on the north side to give you the best protection from the prevailing northerly winds. The big central chimney puts your heat sources inside and allows you to make the most of the heat retention in all that masonry. The only update to build one today is that you might want to open up the floor plan a bit to get the heat distributed, and of course the super insulation. I would go for two smaller stove, one each floor, rather than one big one.
If I was going for central heat with wood I think I would do a boiler with storage... maybe a Garn... and in floor radiant.