This is probably a long-term goal, as the passage of time and the rate at which your dwarves move, work and get hungry or tired currently don't have much of a relationship. But once the day-night cycle starts to matter, it'd be nice to be able to assign some of your workers to a night-shift.
I'm none too sure of the best way to go about this, but I daresay it would be fiddly as all hell to assign dwarves to their shifts individually. Perhaps some sort of percentage slider for each profession, adjustable in increments of 25%? Shift assignments would then be semi-random, but every non-Legendary dwarf should be rotated through the night-shift about once a month, and it probably ought to pay a bit more once the economy kicks in.
As for the military and fortress guard, assignments should have separate priority settings for day and night, and there ought to be a method of waking everyone up in the event of a goblin raiding party or megabeast turning up at night; some sort of 'warning bell' item which wakes everyone, and which can be set to trigger a 'ring bell' job in the event of certain alerts?
Lastly, it would also be nice if levers could have a 'pull at dawn and dusk' option for tasks like raising the drawbridge at night.