Symmetry wherever possible. Conforming with the terrain without including the outer-most wall in the smoothing/engrave. With as many rooms as possible (especially noble), I double-wall for engraving purpose. The front door must be smoothed/engraved.
If possible, or will work best given the situation, sewer system of some sort. Defense-wise, network with mushroom-shaped towers. Farms will always be above-ground on top of underground crops wit farming-related stations nearby, sometimes including a livestock pen. Independant powersources wherever possible (Direct windmill contact with millstones, Aqueducts with individual pump stations per tier at different sections; more time consuming, but tends to look neat, engineering-wise).
Regarding travel and trade, 3-tile wide paths for most of the fort.
NEW:
Thanks to recent developments with my megaproject, I now will claim tree farms, plus, it'll make use of the excess stone.
Notes, they now serve a purpose to me. I'll need them for what does what on my ship.
Oh, and pathing is going into greater detail. Especially regarding tree farms and wood/plant collecting, and even some building projects. Let's keep some flora while building; plus, I'm fed up with some of the path choices made at times. Might as well re-route them.
Oh, and whenever I plan on making command centers and other floating/suspended structures, I'm going with a pretty reasonable/realistic structure method. I mean, bulkheads, doors with blast door floodgates and etc.