I like pits and chasms - if I'm building an underground fort, the entry chamber is usually a pair of bridges connecting to a 5x5 pillar in the middle of a pit that drops down several z-levels. The trade depot is, of course, on the pillar. Often there are carved columns rising out of the pit, with waterfalls flowing out of them. I like to imagine the columns have humongous gargoyle faces on them, mouths open wide to let the water through.
Residential areas tend to be a few z-levels above the workshops, with chasms dug down to the workshop level, so that the smoke from the forges can waft up into dwarves' houses and comfort them as they sleep. Bonus points if they can end in magma as well.
Above-ground forts tend to be big squat castles of local stone, with the underground reserved for storerooms and sprawling tomb complexes. My current fort is planned to be a castle for the nobles, with an attached above-ground village for everyone else. In theory, levers in the castle can be used to seal off sections of the village in case of an attack, and - in a perfect world where I am not lazy - a second set of levers can drop those sections into a fiery abyss. That will be a pain to plan along with a proper sewer system, though.