Well, let's see. In a fully developed fort?
Topside: Entryway, possibly archer tower(s), walled and roofed surface farms. Surface plants are soooo easy.
Soil layer: I try to skip the -1 layer, and if possible -2 as well, because of WET STONE interrupts. If either of those are sand, however, and I have no sand elsewhere, then I make one of those the sand collection zone (doesn't take much). Underground farms and a section for butcher shops, tanner shops, stills, kitchens, and milling. And fish dissection. All food industry exists here, right next to my farms.
Additionally, next to the butcher shops, a mine cart sitting on a single tile track stop, set to dump north. North happens to be a hole leading to magma. The mine cart takes from a refuse stockpile immediately surrounding it. This sets all rotten food, corpses, and body parts (except for bone) to be immediately incinerated.
Next to the stills: a quantum pile containing nothing but green glass pots. From the wiki: "Large pots are currently 2.5 times as heavy as barrels made from the same material, and they have double the capacity." Next to the farmers workshops and milling stones: a quantum stockpile containing nothing but barrels and bags. For flour and syrup, naturally.
Also one layer above this (if possible), a very large stockpile for any and all food items: meat, eggs, tallow, plants, milk... basically anything NOT a prepared meal or a glass pot of booze. Stairs up/down to this stockpile immediately next to the kitchens.
Also on this layer, if I am able: an underground river, re-directed from the topside. Used for fishing of course, runs off the map at the edge. Usually has a drain leading to fall on two statues set into a wall, and then two wells, such that mist is generated but the only path for the water to fall into is via the wells. Below the wells is a cistern, when that fills up there's a corridor that runs the excess off the map.
The rest I purposefully mine out for trees/plants.
Shops and Hall Level, usually the second hard-rock layer I hit (the first being set aside for plumbing). Dining hall, several BIG well decorated rooms for booze just off the hall, and one medium sized prepared food stockpile which borrows from a much bigger overflow pile. All booze should be in glass pots, all full pots should be stored in these rooms. The hall that connects the Meeting Hall to the shops contains the stairwell, and also you must pass by the wells and misters.
The shops consist of five or six quantum piles for raw materials, one for plain furniture and goods, one for masterwork metal furniture-goods-armor-weapons, and one for less than masterwork (this gets melted now and again). Near each of these are the appropriate workshop. All of these are surrounded by walls on three sides, just in case I need to segregate a dwarf and lock him/her in.
The layer directly below this is usually magma (if I've finished the pump stack or piston) and the cistern. Also a quick corridor to a pit to dump prisoners into the:
Military level: Archery ranges, two lanes of ten targets. On the other side, training for the melee dwarfs. On the north side: the arena and landing zone for goblins. On the south side: the hospital, UNLESS I have successfully re-routed the river, in which case it is moved up to a VAN by the RIVER.
After that I leave about 5-8 levels for mining, if there's anything useful in there, and then lay down the bedrooms. Underneath the bedrooms, nobles rooms. Nobles get a small booze stockpile on their level. The rest underneath those, is usually just stairs and magma pumps, and exploratory mining.
I breach the caverns but immediately wall off access; anything I need except for spider silk can be picked up from my farm level. Only on rare occasions do I venture out into them, I'm super paranoid about syndromes and keeping FB goo and blood and dust off my main population, as such I have to engineer elaborate baths and decontamination rooms.