I like the compass/clockwork system I apply to certain setups. Optimization level depends on purpose and setup, I guess. Tends to yield in rather structurally organic fort designs with a chance of geometric prettiness. In a sense, I noticed my forts follow a rather hive-like, yet flowy design structure. In other cases, it also ends up looking like a sophisticated flowchart.
Funny enough, about that, I am now designing forts after the flowcharts I make as their plans. Branching in 3D sometimes (yielding in potential hive-fortresses). Like I mentioned earlier, it's level of optimization depends on purpose assigned, and how it's designed. Excellent examples are
Wavehandle (The best example of a hive cluster would be the trade depot/warehouse) and my latest build (that lost it's first year because I didn't save during, so I'm back to square 1 (fortunately, I already embarked). At least it gives me an opportunity to try again, but a bit more refined and efficient, compared to my last playthrough.
EDIT:
Just as well, first time playing the new version, and holy Armok, I didn't expect chopping a few trees would overstock me on wood supply so fast (first chop through took out a fair amount of fruit trees; now I do conservative chopping to maximize fruit yields, while still collecting). I think building airships can be a signature thing I can do with completed forts now; especially with some building tricks I learned over time, and so on. Being short-stocked on wood was the main issue with building airships; nowadays, it's a trivial matter now; getting the copper (more flexible (higher heat capacities as well) and prettier than iron or steel) supply (boilers) is the next challenge (unless I do the coin-exploit).
Add another to the list, I preserve my environments (no destroying the surface to find materials like gems and rare metals (or copper veins) and such), or try to keep a consistent color pattern through my forts; especially where Stonesense and the like are concerned.
EDIT EDIT:
Started over. Half a year, and everything's working beautifully. Sure, it's not entirely efficient now, but it will be soon enough. However, the flowcharting method of building is working like a charm.
Another thing I do: Dig out a connection to flowing water, and make a fancy watering hole/bar/tavern (Wavehandle has an example). In my latest fort, it's not the primary dining hall (though I do leave a food/drink stockpile in the center of it, and it's surrounded by about 24 seats (chair+table)), but it's more like a social hall. Makes for a good meeting zone. The epic dining hall is elsewhere. This is just a hole in the ground with a water source.