advance warning: All of my examples are going to come from the same fort -- which was made primarily to be tidy, rather than just for efficiency. Some things are made to be massive, instead of just practical. Pardon in advance, I don't have anything else worthwhile uploaded.
Hallway size: I prefer hallways that are at least three wide, personally speaking --
Here are some examples of why. While occasional side-passages that are 2 or 1 square wide are okay, it's a lot easier to make 3-wide halls everywhere on the off chance that you expand your fort out that way later. Having the main hall be 4-5 wide is a nice aesthetic choice, but probably not as efficient.
As for movement between floors... I'm a fan of a
grand central staircase in the very center of a fort, and periodic (every 16-20 squares, ideally) similar stairways all throughout the main halls in the fort. I use up/down stairs in every fort; and have never had a problem with dwarves falling to their deaths. Careful interlinking across Z-levels is really one of the keys to efficiency, I think.
I'm also fond of
modular housing and
compartmentalized refuse heaps that ensure miasma can't spread. Big enough compartments that it saves space; small enough that dwarves don't usually have to venture into miasma.
Trash chutes (although defensively risky) are quite handy for handling a number of issues around the fort, especially the disposal of unwanted items or creatures. For this reason, it's nice to build one's graveyard, refuse pile, and a few butcher shops / tanneries / bonecrafters in the general vicinity of the bottom of the trash chute. Just make sure to zone it such that the dwarves will walk
around the bottom of the chute, not
under it, to avoid crushed dwarves. It's also a good idea to have stairways in this vicinity; because dwarves sometimes get very picky about which floor they want to throw things off of, if they're given a choice.
For trading -- build a
tower and sub-basement above/below your trader's depot, and make sure all (or most) of your saleable goods are stored in that tower/basement. It makes trading much, much faster.
For food -- build
a few stockpiles somewhere near your farms, and have all of your stills / kitchens right beside them for ease of cooking / brewing. Put smaller stockpiles inside dining halls however -- for more efficient eating. It may also help to have numerous small dining halls, instead of one big one. Haven't tested that yet, though.
For water --
All I can say is that it should be near the very center of the fortress, if you want anything to get done.