I decided that dwarfs are likely claustrophiles (the opposite of claustrophobic), when I was first deciding how to design their individual rooms, so dwarfs always sleep with their beds facing atleast 2 sides of stone, and their private quarters almost never have open spaces, or more than 1 space between the raw stone.
Every dwarf (or dwarf couple) eventually gets their own room, atleast 3x3, complete with a pillar of raw stone in the center, and a door for privacy.
I like to design complex labyrinths, so my entire fortress tends to become one huge maze, with multiple entrances and exits. Everything gets guards/traps, but my soldiers go out and fight, or stand guard over workers. They don't hide behind traps, the traps are just there to avenge soldiers and protect against thieves and kid-snatchers.
Fortresses will be enclosed with stone, and guarded. Nobody gets in or out without passing checkpoints.
I always build my fortresses in maximum-size areas, and one of my priorities is building a grand road for the caravan, from the bottom of the map, right to the fortress.
I don't clearcut tree areas, some trees of each type present are always left alone.
I like to build hidden temples, and secret little areas. Even if they'll probably never be used, there will always be atleast a tightly guarded, secret temple to the forge-god, with a working forge.
My captain of the guard gets assigned several war dogs, sometimes all of them, and will be trained up to Legendary in crossbow, even if already legendary in another weapon type . His/her function is basically as a first response problem-solver, aside from the regular army. The Captain goes in first, comes out last, and other dwarf soldiers will gather around the Captain in times of war. The Captain's quarters are always as good as anybody else's, or better, but are designed for function over form, and the toughest dwarf in the fortress gets the job.
Dungeon Masters get not only nice quarters, but a working private zoo, all their own.
Gems stuck into walls that I don't intend to mine out will commonly be left in their raw state. If possible, I like to build my Fortress's main living quarters in a gem area.
Gardens/farms, and animal stocks are continuously guarded by soldiers, even if they're completely safe from attack. No exceptions. If the walls are soil, they'll be lined with cut stone or bronze as soon as possible.
Outside areas will always be incorporated into the overall fortress, and, whenever possible, there will be several tightly guarded water areas.
Garden areas will also, if possible, function as nurseries for dwarf children.
Wounded soldiers, including guard-dogs, are guarded until they get convalescence, or they die.
Legendary dwarfs are always part of the military, and always have solders under them. It's good for the soldiers to see what they're fighting for, and to have good role-models.
Soldiers, even if they have their own private quarters, also get beds in the army barracks. Army gets it's own kitchen, storage areas, etc.
Masterwork items are never sold, and unless they're weapons/armour currently in use, are usually displayed prominently, often in a museum-type area right outside the crafts area, or otherwise in a public area.
Dignified funeral areas are a must, but I tend to make them more communal affairs, with long rows of niches, built around several magnificent central shrines. I'll vary this though, so some dwarfs will get more elaborate personal crypts, when I feel like making them, or feel that a particular dead hero deserves a singular resting place. They may be buried with a palette of collected goblin weapons.
Walls are almost *always* atleast 3 stones thick. Very few exceptions, and these are always done out of absolute necessity.