I like to do a lot of above-ground agriculture, so I usually dig an entrance, run it through the usual trap-, fortification-, and drawbridge-lined hallway, and then tunnel back to the surface inside a wall-enclosed courtyard. I try to always build across a river (despite the occasional alligator fun) so that I can have emergency drawbridge exits to both banks, which is handy when there's a siege on one side of the river but not the other.
The surface level gets the refuse pile and the tanning shop, so I don't have to worry about miasma; a crafts shop for refuse-pile bones, a fishery next to the interior fishing zones, and then a half-dozen farm plots. (I love surface crops so much more than the dwarven ones, since there's none of that seasonal rotation nonsense.) If I've got a river, then the waterwheels go in right next to the farms for easy mill access. Lastly I build a pen next to the tanning shop, rope my breeding cattle in there, and pet-forbid the doors so that I don't end up with calves running all over my meeting hall. I build a floor over the top of the shops to protect them from rain, and on top of that a barracks with fortifications overlooking the main entrance outside the walls. (I like to keep soldiers outdoors and sun-acclimated as much as possible.)
Z-1 is all the stuff that supports the agriculture on the surface level - underground farms, butcher, kitchen, mill, farmer's shop, leather shop, and all the plumbing for machinery and indoor waterfalls on the lower levels.
Z-2 gets the trade depot and all the trade-good-dedicated shops and storage areas.
Depending on how many levels of dirt there are between the surface and the first layer of engravable rock, I cram in industrial burrows however they fit - a furniture/machine burrow, a metal- and glass-working burrow, and a clothesmaking burrow.
The first rock layer gets the grand engraved dining hall, directly underneath the food storage. Underneath it are the grand engraved hospital and grand engraved jails. Underneath them is a water reservoir because they all get wells right away and waterfalls later once I've got the pumps going. The shaft down to the mines runs through the hospital, since that's where most of my recoverable injuries seem to happen. From there it's one more long trap corridor before it opens up for free mining.
Apartments get a reserved area off to one side; everything above and below them is off-limits for everything but residential expansion, to avoid awakening noises.