I build a store room and a farm, get all my embark gear underground. Then I dig a stairwell down, and line it with rooms and workshops, starting with kitchen and still, then mechanic, mason, carpenter, and jeweler. Once I hit enough ore, I build a wood furnace, two smelters, and a forge. Then I build a long defensive entryway and seal up the initial entrance.
I used to build above ground structures, including one giant hollow spike over my fort, (The fortress of CityLions menaces with spikes of dolomite, granite, and clear glass!) taller than any mountain around, but I found I couldn't deal with the mess. Nobody cleans blood above ground, and if you roof in an area, it will never get clean from rain. Citylions was a great fort, with a magma tube 12 z-levels down, but once it hit 5 FPS due to 180 dwarfs and near infinite quantities of blood and vomit, I decided I needed to do something different. Before all the blood, I had 120 dwarfs and 35 FPS. I figure I could get 200 dwarfs and playable FPS if I deal with all the blood.
That should really be the name of the game: "Deal with all the blood!" I suppose that is what Slaves to Armok: God of Blood really means. We really are slaves to the blood god.
Currently, I have been building forts with blood cleaning in mind. My entry hall is looooong, and floodable. I have a recirculating water supply running through a filter grate and under five wells, each set into a nook in the wall, with an atom smasher waiting to come down on the one space dwarfs can stand to clean themselves at the well. My entry hall leads to the corner of the map, a little valley where I've removed all the ramps down that I could, leaving only two ways in. I'm now experimenting with hunting dogs in windowed rooms as non-disposable guard animals. Hunting dogs supposedly have longer site range, we'll see if putting them in a windowed room off the main hall still lets them detect thieves. I'm also trying them behind a window behind a fortification, for ultimate protection. Fewer dead watch animals means less blood.
So, I guess none of those answers fit. I build underground, but I still build defenses. I don't see the benefit of above ground defenses. If I were growing above ground crops, I would build completely walled and roofed enclosures with no entrance except from below ground, like I build for my fisherdwarfs. I also tend to build reactors instead of above ground waterwheels or windmills. Basically, the only thing above ground on my current fort is the fisherdwarf's shack, and a few tiles of flooring covering up the old entrance.
Inside, it's a right mess. Ore bearing walls of rooms get dug out and replaced with block walls, meaning there are strange little passages and cul-de-sacs everywhere. Mined out ore veins get turned into hallways with odd shaped rooms. I like to build vertical forts underground, where everything is in a stack instead of spread out, so the fort isn't very grand looking from the top, even inside.
I guess my answer should be "I try to build forts that maximize FPS by minimizing pathing and contaminants."
By the way, thanks to the grate, my dwarfs are now drawing "water" instead of "stagnant water" from my wells. I don't think the recirculation is necessary, when dwarfs clean, the contaminants don't fall into the well, do they? But I needed a reactor anyway. I think I'll go update the wiki entry for wells, you need a grate in the system if you don't want your dwarfs complaining about water quality.