I tend to "layer" my fortress.
On my current fortress, the outside world is walled off (huge fucking walls, they cover nearly half of a 5x5 map with inner, outer, and far outer walls, with a long moated entrance that is also roaded and trapped, with crossbow towers at key locations.
Outside is just used for farming, trading, and tree collection.
The second layer of my fort (layers go downwards, so first layer is above second) is usually workshop and military stuff. That way, my soldiers can get outside quickly, and haulers don't need to move materials too far to get to the depot or workshops. There is also a well here.
My jail/rancor pit is usually on this level as well.
However, if the second layer is a soil, I use that as a big farm, and then the third would be workshops and stuff.
The third layer, which is usually stone, is my food processing zone. Here, plants are made into booze and food. I'll also fit in smaller workshops such as mechanic's workshop and bowyers workshop.
The next layer down is usually the metal work part of my fort. However, since my current fort has NO metal anywhere, the metal forging is in the third layer.
The fifth layer down is most often the dwarve's sleeping quarters. I make long 2x5 columns of 2x2 rooms, smoothed and engraved for each dwarf. I also put the dining room and another well here.
Below that is the noble's rooms.
Below that is more dwarf quarters.
Below that is the cemetary.
Below this is just mining and core samples, or a pit that goes down many Z levels for getting rid of caged goblins and cats.