Well, I've only really built a single fortress, and then messed around with the starts of a small number of others, largely for the purposes of testing out some modding, but I'm developing some trends in how I make these things. I'm refining my technique more and more towards vertical building.
I like to create a second-story enterance to my fort once I have some more labor and the materials for it, and just wall up my original enterance. Instead of building a moat, I just make a constructed platform, ramps, and drawbridges, which is ultimately faster than digging a moat, since you're just using open air. (If you use multiple drawbridges and platforms, you can still make a "catapult" bridge that dumps people into a pit/labarynth, however.)
I choose one floor to be my "traffic floor". You can, ultimately, just make this one giant warehouse in the soil layer, but that looks a little ugly, and I prefer to have a set of geometric roads of varying width, all smothed, and sometimes engraved as a major traffic hub floor. If this floor doesn't have the warehouses, I prefer to make a warehouse floor, preferably on a soil layer, with each massive stockpile dedicated to a specific industry (food, textiles nearby, stone, gems, metal, wood, etc.) and then a staircase in the middle of the stockpiles where small pods of workshops can be no more than a couple of steps away from a staircase, which itself leads to the warehouse for its type of goods within only 3-5 floors. (Magma workshops are an exception to this rule for obvious reasons. My magma glass workshops (B3) are built upon a linear trough of magma (B4), the floor above them is a warehouse (B2), and the floor above that (B1) has sand, so I just build my sand bagging glass workshops right on top of the sand.
For my residential quarters, I build them right in the middle of the fort. My road floor has a dining hall, and later, a great hall with a zoo and statue garden and waterfalls right in the dining hall. (Haven't actually completed this yet...) The homes are built vertically, just like how most people do them, but I could simply knock down some walls and combine some smaller dwarven apartments together to make my noble's quarters. I tend to go for the dramatic, however, and build my noble's rooms into the cliff face of mountains, especially on the tops of the mountain peaks, where I can make some balconies, or some window-walls to survey the lands before them.
I dig straight down from the residential areas to the lowest floors to make my tombs and prisons. I suppose it might actually be a little faster to put the tombs in the stoneworker's district, since the furniture for it (coffins, cabinets) are generally made of stone, and the prison would probably be best put under the food production district.
The working districts are arranged in a wheel around my residential district, so that I have the most efficiency in transport. I don't exactly make my road system an actual circle with spokes leading to the main residential district, but maybe I'll do that in a future fort. I do, however, have a special "trade depot" warehouse for the trade depot that effectively is its own district. (Since it is near the enterance, it also has my animal stockpiles and kennels, as well as my death pits, halls of death, spikey death, smashing bridge of death, and arrowslits so that my marksdwarves, quartered above it all, can rain bolt-based death upon anything that survives the rest of that crap. It takes up a lot of room.)
I also tried to make a massive "greenhouse" district, so my foresting could be done underground (never go to the surface again), but this wound up being so incredibly consumptive of labor, that I wished I had put it off for several years while I got my magma industry running. Still, it might be worth leaving a large quarter open for expansion in that regard, if you don't have a underground river, or don't want all your wood to be tower cap.
In summation of a long, rambling post, I don't try to divide my fort by Z coordinate, but by X/Y coordinate. Stacking leads to more efficient hauling jobs, and running from the very bottom of the fort all the way to the top will probably take less time than running past a fair-sized warehouse. Running even fifteen floors straight down is like running past only 5 workshops... 4 if you put walls or spaces between the workshops.