I have a main shaft going down a couple levels (I usually leave at least one level completely undisturbed except for shafts, because I like to use collapses as defenses and don't want them punching through the floors). The main shaft enters into a small hallway that connects to another main shaft, this one generally going all the way to the lowest level.
#X#
#X#
#X#
#<..>#
###X#
(and so on)
That little disconnect between the shafts makes it easier to defend (by blocking the hallway there off with floodgates or bars, one can force an invading army to route to a much longer, more dangerous pathway).
After that, I connect to the main shaft with large, open rooms for stockpiles. Past those (or inside those), I build workshops to relate to the goods stored in the stockpile. (One stockpile holds certain items, like plants, fish, and thread, that need to be processed. It'll be surrounded by looms, farmer's workshops, and fisheries. Another stockpile holds meat, processed/cookable/brewable plants, and is surrounded by kitchens and stills.
The pantry is on its own level with nothing else there, and contains two large rooms (one booze stockpile and one prepared meal stockpile). It's generally a level below the workshops, and a level below the pantry, I have a dining room and the lever control chamber.
Basically, I sort everything vertically. On one level, I have farming and most food industry. On another level, valuable production industry (metals, cloth), and on another, bulk production industry (stone/wood/bonecrafting, masonry, carpentry, etc). Those are all clustered together on three or four z-levels. Below that is the pantry, and generally on an adjacent z-level, there's the dining room and the levers. The levers are on the same level as the dining room (just opposite) since that puts them in easy reach of the largest concentration of off-duty dwarves.
As for each level...
The structure I use a lot is thus.
XXXXX
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
. . . . .
XXXXX
Stockpiles connect to that hallway. Only one of those stairways leads out of the fort, but the fact that there's two means that a dwarf doesn't have to tramp all the way across a stockpile area to get some booze. It shortens everyone's paths and keeps congestion down.
As for the rest of the z-levels... I put the bedrooms one or two z-levels up from the bottom of the map, and mine out the very bottom whenever my miners are bored. I use flood traps and don't want to accidentally flood the fort; the open bottom level is a nice drain. The bedrooms are isolated from most noise, though i've been known to place workshops on the bottom level (to take advantage of the ready-to-hand stone piles).