I still follow the style in the Play-Along tutorial that's linked to somewhere on these forums - dig a 3 tiles wide hallway about 20 tiles into the fortress, and put stuff you need there and then on both sides -- indoor stockpiles, a small-ish room to house seven beds, that sort of thing. At the end of the hallway, I put a 3x3 staircase of Down Stairs, and behind that, I've taken to build fortifications with a ballista behind it.
The staircase goes some levels down, to another corridor with Down Stairs and a ballista at the end (and perhaps fortifications on one or both sides, with that can house crossbowdwarves). Once you're past this "checkpoint", the staircase continues down some levels more (at least until I hit rock, though I always have at this point), until it
So the vertical layout is:
Entrance (original rooms are given other uses once the depths are furnished and in use)
|Checkpoint (with ballista or catapult, as well as ammo storage and food and bedding for siege operator)
|| (perhaps even more stuff on the way down, like a hallway that can be flooded with magma or a natural or artificial obstacle with a lever-controlled bridge)
|Stockpiles
Workshops (short way from residential area to workshops, short way from workshops to stockpiles)
Residential (bedding, dining room, food-related workshops, food stockpiles)
Workshops
Stockpiles
|Tombs
|Exploratory mining at lowest floors.
basically first check how many tiles there are until I hit the bottom, and then build the residential level halfway down. Then I start exploratory mining at the bottom, and build a level for burial a couple of levels above that. I try to make it so that the defences on the way up are only accessible from deep within the fortress -- instead of there being a door leading the ballista at the entrance level, there will be a staircase going down to the residential area, and this staircase will be the only way to the ballista.
Each floor is symmetrical, built outwards from the central staircase. I don't think I'll ever need more than one floor each for Residential
A way to dispose of excess stone, litter and junk.
You can do what the play-along tutorial suggests - dig a shaft from the surface to the refuse stockpile, making sure to make a wall around it at its top so enemies can't fire down it. Miasma will escape up into open air.