I always use the GnomeChomsky's Tessellated Apartments from the wiki, stacked one upon another, with some adaptations.
Surface - Trade Depot, finished goods stockpile (on bins)
Z-1 - Farms and seed-only stockpile, no barrels
Z-2 - Farmer's Workshop + Looms, and empty barrel + cloth stockpile (on bins)
Z-3 - Clothier + Kitchen + Still + Butcher, and food stockpile taking only dwarven syrup + cloth stockpile taking only cloth from the stockpile on Z-2
Z-4 - Ligth workshops, like carpenter with an small wood stockpile, mason and mechanic's with a stone quantum garbage zone, and crafter with refuse stockpile set only to take bones, skulls and shells. A furniture stockpile, excluding bags and barrels, taking also blocks.
Z-5 - Dining hall, with a drinks-only stockpile in the outlying small rooms, taking from the stockpile on Z-6
Z-6 - Food and drink stockpile, taking all except seeds, plants and syrup
Z-7 - Drink stockpile and food stockpile taking only cooked meals
Z-8 to Z-10 - Rooms
Z-11 - Empty area for miscellaneous storage or occasional workshops (jeweler, leatherworker). If I am in a map with sand, for instance, I use this area to hold only empty bags and sand bags.
Z-12 - Minerals ready for smelting
Z-13 - Magma Forges, normally 4 smelters, 2 forges and 2 glass furnaces, and a bar stockpile.
Z-1 (Farms) looks like this:
W=Wall
X=Up/Down Stair
1, 2, 3, 4= Distinct farm plots
s= Seed stockpile, barrels set to zero
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I use a rotating pattern for planting, letting always one farm plot to rest each season. If I want to be extremely picky, I plant one type of crop exclusively in a given plot, and I set the nearest seed stockpile to that type of seed only.
I farm pig tail for alcohol and thread, cave wheat for alcohol, sweet pod for alcohol and syrup and plump helmet for alcohol and food.
Z-2 (Farm Processing) looks like this:
F=Farmer's Workshop
O=Loom
Q=Plant Quantum Stockpile
b=Furniture Stockpile, Barrels and Bins only
c=Cloth Stockpile
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The produce of the farms above goes to the Quantum Stockpile. This is a one-tile food stockpile set to take only plants, zero barrels, and a refuse zone on top of it. I don't have any other plant stockpile on the whole fortress so, when one of the farm plots has been harvested, the plants remain there, blinking. When all the plants in a plot have been harvested, I mark them for dumping and they end in the Quantum, safe from spoiling. It is important to set this zone inactive when dumping anything else (see below).
Every plant goes here and gets processed in this level or the next one. Here, pig tails are turned into thread, and sweet pods into dwarven syrup. In this level the thread is also processed into cloth.
All the seeds, by-product of the processing go to the stockpile above, conveniently close.
The outlying L-shape rooms are useful for non-processable refuse (chunks and dead vermin) or other miscellaneous and transitory need.
Z-3 (Food, Drink & Clothes) looks like this:
Z=Kitchen
L=Still
K=Clothier
y=Dwarven Syrup Stockpile
c=Cloth Stockpile, accepting only cloth and taking from the cloth stockpile above
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The dwarven syrup produced above is cooked here into roasts, to be sold each stack by 25,000 monies or more to traders. Note that when the syrup is cooked and the barrel holding it is emptied, the barrel is hauled back upstairs, to be reused.
The still here takes plants from the Quantum and barrels' stockpiles above (or from the kitchen if both operations are on at the same time and the haulers are not fast enough to clear the kitchen of used barrels), and produces alcohol. Seeds go just to steps upwards and a few more to the stockpile by the farms. The alcohol-filled barrels are moved deeper in the fortress.
The clothier's workshop just takes from the cloth-only stockpile and produces any piece of cloth or bag as needed. They can go to a finished goods stockpile taking only cloth items, set in the nearby L-room.
The empty 3x3 area can be used for a related industry, for example dyeing or butchery, the adjacent L-room set to dye or animal stockpile, respectively.
Z-4 (Light Industry Workshops) looks like this:
M=Mason
C=Carpenter
R=Crafter
T=Mechanic
u=Furniture Stockpile (no barrels, no bins) combined with Block Stockpile
w=Wood Stockpile
Q=Quantum Garbage Zone
r=Refuse Stockpile taking only bones, skulls and shells and corpses
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The Quantum Garbage Zone receives all dumped stone produced by my miners. It is turned into furniture, blocks, crafts or mechanisms in the nearby workshops.
It is important to keep this zone inactive when dumping anything else (i.e. plants from the farms).
The carpentry churns out barrels and bins on demand, that get used immediately for storage, or moved upstairs to the bin-barrel-only stockpile.
Note that the miasma produced by the rotting corpses on the refuse areas don't spread diagonally out of the L-rooms. No doors needed.
Z-5 (Dining Hall - Meeting Area):
D=Door
d=Food stockpile, drinks only
T=Table
C=Throne
S=Statue
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Dwarves relax and drink here, their alcohol conveniently at hand.
This drinks-only stockpile takes from the storage area immediately below.
The doors and walls define a Dining Room area that can be smoothed, engraved, laid on gold blocks or decorated with statues or artifact furniture, to reach Legendary quality.
Z-6 (Food & Drink Storage):
This level has exactly the same shape as the others, but all the open space is half a food stockpile taking all except syrup, plants, seeds and cooked food, and half a food stockpile taking only cooked food, no barrels.
The Dining Hall drinks' stockpile above takes from this, and the dwarves can just step downstairs for their pick of cooked meal.
Z-7 is the same as above.
Both levels, full of food and booze can last years.
Z-8 to Z-10 - Rooms
Note that two levels of food storage above provide enough noise insulation from the workshops further up.
W=Wall
D=Door
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X= Up/Down Stair
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And every individual L-room is furnished like this:
B=Bed
H=Chest
C=Cabinet
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This packs 16 dwarves per level in individual rooms.
Different levels of smoothness/engraving and furniture quality provide the necessary room quality level.
I try to house the upper industries workers on the Z-8, haulers on Z-9, and lower industries workers on Z-10. For example, the Mason on Z-8, and in a room adjacent to the stairwell also adjacent to the Masonry.
Z-11 and Z-12 are generic storage space, same shape as all other levels. I keep here sand bags, gems or minerals, to be used in the lowest industry. Occasionally, they house a Tanner, Jeweler, Leatherworker or other odd workshops.
Z-13 (Heavy Industry) looks like this:
S=Magma Smelter
F=Magma Forge
G=Magma Glass Furnace
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Smelters are feed by the ore in storage above.
The central area is taken by a bar stockpile, which fed the forges.
The product of the forges -furniture, weapons, armor- is immediately put to use in rooms, or the military. Metalcrafts go to the storage area in the surface level.
Z-14 has a branching magma tunnel feeding the forges, connected to the main magma supply in the map.
For the military and nobility, I usually stack 4-5 floors on the Z+ levels, separating the L-shaped outer rooms in individualised towers, Isengard-like.
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Or
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For example:
Z+1 is a Fortified Marksdwarf Station, with Archery targets and bolt stockpile
Z+2 is Training barracks
Z+3 has four state bedrooms, one each for mayor, sheriff, or any other noble
Z+4 has four dining rooms
Z+5 has four offices
Then I add other features to this framework, like a perpetual motion engine in a mined-out mineral vein adjacent to the stacjed tower, or a underground tree farm in an adjacent mined out magnetite deposit.