I may wind up changing my basic design soon because of stuff in this thread, but what I typically do is:
- (optional) 5-wide ramp down to temp farm/living area with room for a temp depot, if I'm expecting my final depot location to take a while.
- Exploratory 2x2 or 3x3 stairwell down a couple z-levels, mostly to figure out if there's an aquifer in the area.
- If area looks good, 5-wide main entry will run past that stairwell, but I don't dig it all yet; I plan it out, with a couple twists, and figure out where the (real) depot is going to be; leave a 9x9 area for the depot.
- L-shaped stairwells bracket the depot at the corners; need about 12 to 16 z-levels.
- 3-wide hallway makes a square around the stairwells.
- Workshops and bedrooms are around the perimeter of the hallway.
Currently, I'm doing bedrooms as 5x9 areas with a 2x3 "room" in each corner and two "dining rooms" of one table and one chair each in a line down the middle of the large room. I don't do any pre-testing of vampires, so I figure four dwarves eating and sleeping in the same room is a good security measure. I can put 12 of these rooms on one level, for a total of 48 beds. On residential levels, the central area surrounded by the stairs is dug out to form a food stockpile.
Workshops go on another level, non-food stockpiles on the level above or below. Where these are depends a lot on where my soil layers are, and how many there are. I want those for farms and (eventually) underground pastures. An ideal arrangement is depot level, finished goods level, workshop level, raw materials level.
Forges and smelters go on another level, with ore and bar/block stockpiles above. If I have a volcano, I used to put magma channels below, with floodgates to prevent magma flooding the fortress. However, flooring over a volcano seems to be a better plan. On the other hand, if I dig spiral ramps down many z-levels, I could put the depot below the magma channel and flood it as a last-ditch defense.
Once I have a comfortable amount of work done on the fortress and I'm producing necessities and exports, I go back to the exploratory 3x3 staircase and dig way down to find the caverns. This way, if anything invades from the caverns, it goes through the same defenses as surface invaders. I usually dig out at least one area of underground pasture before I breach the tunnels, to get it filled with moss and fungi as quickly as possible.
I've only pierced an aquifer once. I usually pick embarks where I can go around them, so that's an as-yet undeveloped skill. I might have to modify my plans to get something like the central waterfall mentioned above; I haven't worked much with mist, so it's intriguing.