I personally take pride in planning out the layout of my fortress before I go, so my design methods are never organic in appearance past the soil-based floors of the map - always they look pre-arranged, because they are. When I start a fort, I'll drill out several nice wide rooms on all the soil floors just to get space for farms, workshops and stockpiles, then pause and spend the next few days (of real-life time) arranging my first 4-5 floors of stone development so it's all perfect when I'm ready to proceed. Every hallway worth mentioning in my end design is 3 tiles wide if not more. The design always builds around a massive center stair shaft that passes directly through the dining hall, which is typically a few floors below the first z of stone that I find - I don't like leaving it too close to the surface; gives me no room to work above it for cool landscaping features like waterfalls. At least for the first few floors of stone, it's only one kind of business at a time. The floor with the dining hall will also have stuff like the hospital and other multipurpose rooms/buildings. Floors of workshops are only workshops, with floors of only stockpiles above and/or below. Floors of bedrooms are only bedrooms. I find the idea of putting bedrooms on the same floor as a dining room full of gregarious dwarves rather unappealing for those who are trying to sleep, so the bedrooms are usually fairly low down. Fast transfer between floors is facilitated by loads of staircases, and once I have a lot of them I start placing hatches to avoid falls.
Also, a strange habit of mine from my first few games of DF: I almost always open a fort by placing down staircases on open land, never by digging into the wall of a mountain on ground level. Makes it pretty difficult to get the caravan underground, yeah, so I don't even try. Instead, I usually compensate by staking out a lot of the ground around my entrance zone, on the surface level, and bringing it under direct military control; the enemy is never supposed to even get close to the staircases that I start at and it's in these aboveground regions that I plant my trade depot. Having safe access to the surface has a lot of benefits in terms of space to build and gives piles of room for megaprojects and archery training towers (in my last fort, all my barracks were built in a green glass tower in the sky, rising over the central staircase of the fortress below). I had a megaproject planned where I would build a gigantic gate (inspired by
this beauty - i can share the design if anyone's interested =P), composed of eight primary tower chambers rising up to 11z into the air, and connected to a ring of fortified walls all around my fortress. It would be big enough for a wagon to EXPLORE in, never mind walk through. It was glorious and I intend to reproduce it now that we have a new version of DF.
As for interior design, I have only two specific requirements: dense (but not cramped - a fine line), and scalable. I'm very good at getting the first one down but getting the second one has been quite difficult in the past. On my first fort, I had one loooong hallway with a workshop on either side running down a very long distance - not scalable at all, so I resolved to fix that on my next fort. My bedroom layouts are primarily inspired by
this design, which I expanded into a larger preplanned complex. The workshops are based on a scalable 16-shop square of my own making (can replace four shops in the center with one large 5x5, siege or kennel ofc). All output stockpiles go on floors above or below the shops - my design patterns are too dense to put them on the same floor. I use quantum stockpiles to position the input goods if they're raw materials like wood or stone; stockpiling those things is frankly not worth the space it consumes. I also plan out the positioning of the shops themselves to make sure I know where the input and output will go - as always, input is more important than output. Every workshop must be sequestered by doors, individually from all other workshops - none of this combining workshops in a single room business for me; the singular separation gives me a satisfying sense of security.
I always embark on maps with a river (sourced water is just too important to me, and fishing is also nice) so I always construct a cistern off the river and pipe water under the sections of my fortress. For the next fort I make, I'm just gonna run the cistern super-deep, and leave one massive hole running all the way up my fortress - on every floor over that hole, I'll build a well. (It's gonna suck for any dwarf that falls into the hole though. too bad for them)
And as for defense, I take inspiration from the work I see on this forum/the wiki, and any cool architecture I find online that I can build a megaproject out of. I'm planning on combining
this lava trap by Icebird (the trap basically contains a cistern of magma suspended over the entrance hall by a retracting bridge, and the hall flooring is made up of floor grates into another cistern below, then the two cisterns are connected by pump stacks. at the pull of a lever, the bridge above pulls away, dropping delicious magma onto intruders and through the grates into the tank below, which pumps it back up to the top) with the gigantic gate+wall design I had from before. Whenever I get bored I just go fishing for some cool real-life architecture to model another megaproject on, and if the current one is any indication, ancient history is an awesome place to get ideas.
My military training always takes place above-ground, in buildings that I construct. That also includes training of siege weapons. At the top of my old archery tower were a set of catapults, 7z in the air, where I trained my siege operators, with barracks and archery rooms below. There was the obvious risk of falling down the stairs during wrestling, straight through to the bottom of the fortress, which I disregarded for the purposes of fun. The exception is at the start of the game, when I don't yet have the industry to produce those buildings for another year or so. I leave the barracks on the floor right under the entrance to the fortress, right in the staircase room. Enemies then have to walk through my military before they can reach the stuff below, which is reasonable security for the ambushes of the first few years while I build my towers everywhere. Once I have my setups built, I just surround every entrance to the fort with trap-laden paths (menacing spikes, spiked steel balls and serrated disks are where it's at. spikes are all connected to a water/pressure plate repeater design I found on the wiki) that are 10-15 tiles long. More than enough to solve most of my above ground problems.