My process:

1) Think about a floor plan. Some things are really hard to add later (like basements)
2) Use core wood beams or stone blocks to lay out the foundation
3) Build the frame (using core wood, stone, or wood-iron depending on what I'm doing)
4) Build the roof
5) Repair everything that got wet
5.5) Dig out the basement if I'm building one, being mindful not to let the roof collapse
6) Build the floor
7) Build the outside walls
8) Build the inside walls
9) Add stuff inside