For a long time (about half the time I've spent on the 3D version of DF) I'd make my fortresses on a single Z-level, since this seemed to drastically reduce pathing lag. I've always been a bit of an FPS whore, I pretty much give up on a fort if it's consistently under 30 FPS or has massive lag spikes. Lately though with 40d3 - d9 I've built forts that used the Z level again, and my current fortress is heavily standardized in that regard.
The concept is that it's a tower that will be dug out from the ground (with concentric rings of ramp-cut terrain going deeper and deeper to expose more of the tower, bit like a crater), so that the dwarves will all live in the tower and if I tell them to stay inside, they'll stay in the tower. They'll occasionally complain anyway, even when every part of their task is located indoors, but 99% of all work continues uninterrupted during a siege.
The main block is a 11x11 (or whatever a shift-diagonal arrow gets you) room, in the middle 3x3 square I have a single-file line of up-stairs, a space between them, and then a single-file line of downstairs, and these will alternate each level. So:
<<< >>>
. . . and . . .
>>> <<<
I carve out additional 5x5 rooms around this in a standardized pattern. At each corner of the main 11x11, starting 2-squares in (diagonally), I dig out a 5x5 room. It comes out looking like a very chubby X. 1 room is also made in each cardinal direction by digging out a 5x5 block between the gaps left by the corner rooms, connected to the main chamber by doorways. I can exclude areas from being excavated to leave natural walls wherever they need to be, or connect it all into one massive chamber for storage.
One concept I was toying with was to leave 9 8 columns of rock un-excavated around the 5x5 open section that has the stairs in the middle. Between each column would be a 2-square gap, small enough to seal with doors and provide a modicum of protection. It would also allow any level to be independently cut off by locking all those doors, without blocking the dwarves on the other z-levels from using the stairs.
Eventually of course I had to create tunnels leading out of the tower-block for exploratory mining, and I also have a couple of horizontal shafts carrying magma and water into the tower (dangerous I know!). As time goes on I'll probably dig out under the magma and water shafts so they hang in the air like aqueducts, and I can seal up the mining works before I ramp down that far and then reconnect the fort and the mines deeper down. So far only 6 (inside, subterranean) levels of the tower are exposed on the outside, with five more levels dug out below.