I'm working on an aboveground desert fort, at the moment. I've got three levels of soil above rock (no aquifer), and have piped the river into an enormous pond at the center of my fortress.
Ground level is buildings, as are aboveground Z-levels. Usually four workshops to a floor, or two on two separate floors if I'm feeling like it. Every building has doors; all down stairs have hatch covers. The nobility and seven founding dwarves live in a large building positioned over the lake; since I built pumps to cause waterfalls off the sides of the building, it was quite easy to build drowning-chamber plumbing for the nobles. So I did.
The first two underground Z-levels around the rest of the fortress are for stockpiles for the workshops above them. There tends to be a problem when the stockpiles have to be bigger than the workshops' buildings, but I usually wedge housing in between them, with enough of a buffer that there aren't noise complaints.
The third underground Z-level is the "subway". Lots of tunnels going everywhere; every building in the fortress is connected via these. The main barracks is actually at the center of this, underneath the nobles' building--it's the only place dwarves actually sleep underground. All the other barracks locations are aboveground, usually right by their lookout tower to which they're assigned. All of the buildings are also connected through ramps and walkways that go over the streets. It's gotten to the point where some dwarves almost never touch the ground, because their housing, workshops, and dining rooms are all reachable via the underground tunnels or the walkways over the streets.
The biggest problem has been making a suitably awesome dining room to keep up morale, but my metalworker got good enough to bust out a couple aluminum statues and life's been good.