In my current fortress, I'm going for:
1) Entrance Zone. Exists purely as a means for sorting out various entrant groups from each other, from which they can go into any of areas 2-4, depending on which group they belong to.
2) Migrant Zone. Small housing/farming/brewing area used to hold migrants until I get around to putting them in a useful job and housing them properly. Only connects to the fortress proper when I'm letting migrants in.
3) Trade Zone. Contains the depot and vast stockpiles to hold stuff for it. Is either connected to the surface or to the fortress proper, rarely both.
4) Upper Defence Zone. Contains a whole variety of magma related traps, ballista/catapult corridors, archer bombardment lines, long twisty corridors and a permanent, rotating military group. Eventually leads to the fortress, purely because I like to have some possibility of something getting through.
5) Central Zone. Essentially a massive spiralling access system linking up all internal sections.
6) Actual Usage Zones. Contain various industries, housing and the like.
7) Lower Defence Zone. Attached to the bottom of the Central Zone. Essentially the same as the Upper Defence Zone, but links to the caverns instead.
Internal Defence Zone. Another layer of security and stuff, with the secure zone behind it.
9) Secure Zone. Contains stuff I really don't want getting attacked. Will probably be turned into a (smaller) copy of the central zone eventually. Has the jail and stuff coming off it. Also contains the control room, behind another layer of security.
10) Surface Zone. Closed off by a wall from the rest of the surface, for farming, herb gathering, woodcutting and the like. Also has a small defences base behind it, and the capacity to seal it entirely, in case of flying attackers.
11) Cavern Zone. As Surface Zone, but entirely walled off from the rest of the caverns.
Each individual zone can be separately sealed off from the rest of the fortress from the control room, and there is a separate set of corridors linking the internal zones without going through the central zone that are usually sealed. I occasionally lose a couple of zones to attacks, but I've yet to lose anything significant.