My forts tend to be strongly layered, going double on flatter embarks. The surface level consists of multiple rings of walls, with moated drawbridges and a metric ton of (cage) traps if possible The butcher's shop, tannery, and refuse stockpile are also out here, safely walled in. Below it comes an entrance layer with a long hall and the trade depot. Soil layer(s) are dedicated to farming, sand collection, and related tasks. The first stone layer is the "war" layer with barracks, archery ranges, kennels, and when I reach that point my mass pitting top room, hospital, and jail. The next layer down is the hoard, consisting of all non-food stockpiles, usually with a handy little bolt-recovery room. the following layers come in a sort of random order...
> Workshops, with quantum stone-and-goblinite stockpile
> Living quarters, either just masses of 1x3 bedrooms or combined with...
> Food processing: dining rooms, food/booze stockpiles, kitchen, stills.
> Noble's quarters: Slightly larger bedrooms, all mission-critical levers (near the stairs), offices, and a drawbridge death-chamber that I always build but never use.
Crypts are at the bottom of my "active" fortress. As soon as accommodations for the living are online, my masons ensure every dwarf's hereafter is prepared for with a sarcophagus and door to put it behind. Tombs for dwarves that achieve something special, and noble tombs may also be carved out on this floor.
Below the crypts, things vary wildly, and embarks can change the whole plan: a recent steep volcano embark featured a dedicated furnace layer with ONLY smelters, forges, glass furnaces, kilns, and their related stockpiles, with a dedicated magma layer beneath to power them
It's been a brief learning process so far, but one with much fun already: the crypt layer, for instance, only appeared after an "Endured the rotting of a friend/loved one" based tantrum spiral.
My current best fortress (Ironbear, for which I think there's a story, save that the end remains unwritten) I've got the war leader of the local goblin civ in a platinum cage, and it's over 200 dwarves and, unfortunately for them, boringly well-managed. They might be in for a semi-megaproject soon. Ziggurat over the entrance? Magma mine so I can stop clear-cutting the formerly "heavily forested" overworld?
Or perhaps I could widen the main roads so I stop having dwarf traffic jams in the long, twisty 1-tile-wide passages... nah.