It depends how I want to play. Most fortresses I just enjoy smacking goblins and other invaders around with military. That's a straight-forward cubic castle going down into the ground 5-6 z-levels. A very simple approach like that seems to minimize fps loss from pathing. Each floor has a specific use - ground floor is for training, clay floor is for stockpiles, first stone layer is a workshop floor, next one down is for magma plumbing, next one down is sleeping quarters, then a few empty ones, then dining room and other niceties on the bottom floor.
If I want to build a true fort I take the time to build specific areas for different modes of productions. The fortress becomes divided into sections, each intended to serve a certain production (metal, crafting, carpenting and so on). Food haulers make sure that food is brought from the farming areas to the other ones. Each section includes a local dining room, a small hospital and so on. These fortresses tend to be significantly larger vertically speaking than the military fortress. This will leave room for rooms that aren't really necessary, but nevertheless awesome to have - like breeding rooms, tower cap farms, prisons with lots of FUN, arenas and so on. Unfortunately, all this stuff means a dramatic loss of FPS, and as such I really don't enjoy playing them for too long.
Easily the most impressive fort I built was on top of a volcano that had once risen above the ground, but was now hollow to several z-levels below ground level. I proceeded to build my fortress on top of the volcano. The top three floors were all part of a defense grid where invaders had to dodge traps and marksdwarves while navigating across a grid of floors. If the invaders dodged or were knocked back by macedwarves, they would fall down into the volcano, or on built spikes, or into pits of scorpions, or ponds slowly filling with magma after they landed. Of course, the defense was equally deadly for my dwarves, and lots of fun was had.